1
|
Cheng J, Zhou J, Kong L, Wang H, Zhang Y, Wang X, Liu G, Chu Q. Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation. RSC Med Chem 2023; 14:2496-2508. [PMID: 38107173 PMCID: PMC10718590 DOI: 10.1039/d3md00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/19/2023] Open
Abstract
Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.
Collapse
Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Junlong Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
| | - Lingyan Kong
- College of Food Science and Engineering, Nanjing University of Finance and Economics Nanjing 210023 China
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University Nanjing 210009 China
| |
Collapse
|
2
|
Ogasawara S. Replication-competent influenza virus with a protein-responsive multiplication ability. N Biotechnol 2023; 77:100-110. [PMID: 37586547 DOI: 10.1016/j.nbt.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 07/30/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Applications of influenza A viruses (IAV) for virotherapy and biotechnology have accelerated substantially with the development of reverse genetic technology and advances in the understanding of packaging signals. While the use of a replication-competent IAV is particularly promising, owing to its efficient transmission to organ depths with high infectivity, there is also a risk that its multiplication cannot be controlled in a cell-type-specific manner, causing an infectious disease. Therefore, here a simple and effective replication-competent IAV-based cell-targeting system has been developed. It was demonstrated that the activity of the ribonucleoprotein complex (RNP) of IAV could be regulated by the interaction between the endogenous protein and a nanobody fused to the subunit of RNA-dependent RNA polymerase (RdRp). To validate the feasibility of the method, it was demonstrated that RNP containing RdRp fused with Nb139, a nanobody against p53, is inactive in HEK293T cells expressing endogenous p53, but active in p53-defective Saos-2 cells. Finally, a replication-competent IAV was successfully generated that multiplies only in p53-defective tumor cells and an IAV vector was developed that can deliver a foreign gene in cell type-specific manner. The method is flexible because the nanobody can be easily altered to target a different cell type, offering a valuable platform for virotherapy and biotechnology.
Collapse
Affiliation(s)
- Shinzi Ogasawara
- Department of Biology, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.
| |
Collapse
|
3
|
Komar AA. Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics. Molecules 2023; 28:2383. [PMID: 36903628 PMCID: PMC10005171 DOI: 10.3390/molecules28052383] [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: 02/11/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation.
Collapse
Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; ; Tel.: +1-216-687-2516
- Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| |
Collapse
|
4
|
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: 1] [Impact Index Per Article: 0.5] [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.
Collapse
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
| |
Collapse
|
5
|
Zhang J, Xu H, Wang B, Zhang X, Fu L, Li Y, Wu G, Zhao Z, Liu L, Yang T, Zhang Z, Yang J, Jiang T, Qiu P, Yu R. In silico design of anti-tumor mini-protein targeting MDM2. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
6
|
Ramanayake Mudiyanselage TM, Fujiwara D, Michigami M, Watanabe S, Ye Z, Uyeda A, Kanegi R, Hatoya S, Fujii I, Sugiura K. Generation of molecular-targeting helix-loop-helix peptides for inhibition of the interaction between cytotoxic T-lymphocyte-associated protein 4 and B7 in the dog. J Vet Med Sci 2022; 84:1101-1107. [PMID: 35753760 PMCID: PMC9412056 DOI: 10.1292/jvms.21-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Blocking the interaction between CD28 and B7 by cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is a potent immune checkpoint that prevents damage to host tissues from excessive immune responses. However, it also significantly diminishes immune responses against cancers and allows cancer cell growth. This study found that recombinant (r) human (h) CTLA-4 specifically binds to canine dendritic cells (DCs) and suppresses the responses of canine T cells to allogeneic DCs. ERY2-4, a peptide targeting rhCTLA-4 selected from a yeast-displayed library of helix-loop-helix (HLH) peptides and improved to have a binding affinity to rhCTLA-4 as strong as that of rhB7, inhibited the binding of rhCTLA-4 to canine DCs. Furthermore, the targeting peptide significantly enhanced the response of canine T cells to allogeneic DCs. These results suggest that the CTLA-4-targeting peptide enhances canine T cell activity by blocking the interaction between canine CTLA-4 on T cells and canine B7 on DCs. This study demonstrates the generation of a new type of immune checkpoint inhibitor, which may be applicable to cancer therapy in dogs.
Collapse
Affiliation(s)
- Tharanga Mr Ramanayake Mudiyanselage
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University.,Present address: Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Ruhuna
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
| | - Shunichi Watanabe
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Zhengmao Ye
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
| | - Atsuko Uyeda
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
| | - Ryoji Kanegi
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Shingo Hatoya
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
| | - Kikuya Sugiura
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| |
Collapse
|
7
|
Zhou Y, Zou Y, Yang M, Mei S, Liu X, Han H, Zhang CD, Niu MM. Highly Potent, Selective, Biostable, and Cell-Permeable Cyclic d-Peptide for Dual-Targeting Therapy of Lung Cancer. J Am Chem Soc 2022; 144:7117-7128. [PMID: 35417174 DOI: 10.1021/jacs.1c12075] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of peptide drugs in cancer therapy is impeded by their poor biostability and weak cell permeability. Therefore, it is imperative to find biostable and cell-permeable peptide drugs for cancer treatment. Here, we identified a potent, selective, biostable, and cell-permeable cyclic d-peptide, NKTP-3, that targets NRP1 and KRASG12D using structure-based virtual screening. NKTP-3 exhibited strong biostability and cellular uptake ability. Importantly, it significantly inhibited the growth of A427 cells with the KRASG12D mutation. Moreover, NKTP-3 showed strong antitumor activity against A427 cell-derived xenograft and KRASG12D-driven primary lung cancer models without obvious toxicity. This study demonstrates that the dual NRP1/KRASG12D-targeting cyclic d-peptide NKTP-3 may be used as a potential chemotherapeutic agent for KRASG12D-driven lung cancer treatment.
Collapse
Affiliation(s)
- Yunjiang Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Mei Yang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaohao Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huiyun Han
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Chang-Dong Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
8
|
Zorko M, Jones S, Langel Ü. Cell-penetrating peptides in protein mimicry and cancer therapeutics. Adv Drug Deliv Rev 2022; 180:114044. [PMID: 34774552 DOI: 10.1016/j.addr.2021.114044] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022]
Abstract
Extensive research has been undertaken in the pursuit of anticancer therapeutics. Many anticancer drugs require specificity of delivery to cancer cells, whilst sparing healthy tissue. Cell-penetrating peptides (CPPs), now well established as facilitators of intracellular delivery, have in recent years advanced to incorporate target specificity and thus possess great potential for the targeted delivery of anticancer cargoes. Though none have yet been approved for clinical use, this novel technology has already entered clinical trials. In this review we present CPPs, discuss their classification, mechanisms of cargo internalization and highlight strategies for conjugation to anticancer moieties including their incorporation into therapeutic proteins. As the mainstay of this review, strategies to build specificity into tumor targeting CPP constructs through exploitation of the tumor microenvironment and the use of tumor homing peptides are discussed, whilst acknowledging the extensive contribution made by CPP constructs to target specific protein-protein interactions integral to intracellular signaling pathways associated with tumor cell survival and progression. Finally, antibody/antigen CPP conjugates and their potential roles in cancer immunotherapy and diagnostics are considered. In summary, this review aims to harness the potential of CPP-aided drug delivery for future cancer therapies and diagnostics whilst highlighting some of the most recent achievements in selective delivery of anticancer drugs, including cytostatic drugs, to a range of tumor cells both in vitro and in vivo.
Collapse
Affiliation(s)
- Matjaž Zorko
- University of Ljubljana, Medical Faculty, Institute of Biochemistry and Molecular Genetics, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Sarah Jones
- University of Wolverhampton, School of Pharmacy, Faculty of Science & Engineering, Wulfruna Street, Wolverhampton WV1 1LY, UK.
| | - Ülo Langel
- University of Stockholm, Department of Biochemistry and Biophysics, Svante Arrhenius väg 16, 106 91 Stockholm, Sweden; Institute of Technology, University of Tartu, Nooruse 1, Tartu, Estonia 50411, Estonia.
| |
Collapse
|
9
|
Hong SH, Nguyen T, Arora P. Design and Synthesis of Crosslinked Helix Dimers as Protein Tertiary Structure Mimics. Curr Protoc 2022; 2:e315. [PMID: 34982512 PMCID: PMC8740631 DOI: 10.1002/cpz1.315] [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] [Indexed: 01/03/2023]
Abstract
Crosslinked helix dimers (CHDs) are synthetic tertiary helical structure motifs designed to modulate interactions of proteins with binding partners. Helix dimers serve as mimics of coiled coils, which are known to be implicated in a multitude of protein complexes. Coiled coils are typically stable in long peptides (>21-28 residues), because sufficient intra- and interstrand contacts are not available in short peptides to coax strand assembly. To engineer conformationally stable CHDs in short sequences, we introduced a covalent linkage in place of an interhelical salt bridge and sculpted the helical interface with optimal hydrophobic packing. CHDs have shown efficacy for the disruption of targeted protein-protein interactions in biochemical, cellular, and animal models. This article describes our optimized approach to design and synthesize parallel and antiparallel helical tertiary structure mimics. Synthesis of CHDs involves conjugation of individual peptide segments, purification of the mono-conjugated strand, and alkylation of the two independent strands to yield crosslinked dimers. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Protocol for bis-triazole CHDs Basic Protocol 2: Protocol for dibenzyl ether CHDs.
Collapse
Affiliation(s)
- Seong Ho Hong
- Department of Chemistry, New York University, New York, New York
| | - Thu Nguyen
- Department of Chemistry, New York University, New York, New York
| | - Paramjit Arora
- Department of Chemistry, New York University, New York, New York
| |
Collapse
|
10
|
Nagano Y, Arafiles JVV, Kuwata K, Kawaguchi Y, Imanishi M, Hirose H, Futaki S. Grafting Hydrophobic Amino Acids Critical for Inhibition of Protein-Protein Interactions on a Cell-Penetrating Peptide Scaffold. Mol Pharm 2021; 19:558-567. [PMID: 34958576 DOI: 10.1021/acs.molpharmaceut.1c00671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Stapled peptides are a promising class of conformationally restricted peptides for modulating protein-protein interactions (PPIs). However, the low membrane permeability of these peptides is an obstacle to their therapeutic applications. It is common that only a few hydrophobic amino acid residues are mandatory for stapled peptides to bind to their target proteins. Hoping to create a novel class of membrane-permeable PPI inhibitors, the phenylalanine, tryptophan, and leucine residues that play a critical role in inhibiting the p53-HDM2 interaction were grafted into the framework of CADY2─a cell-penetrating peptide (CPP) having a helical propensity. Two analogues (CADY-3FWL and CADY-10FWL) induced apoptotic cell death but lacked the intended HDM2 interaction. Pull-down experiments followed by proteomic analysis led to the elucidation of nesprin-2 as a candidate binding target. Nesprin-2 is considered to play a role in the nuclear translocation of β-catenin upon activation of the Wnt signaling pathway, which leads to the expression of antiapoptosis proteins and cell survival. Cells treated with the two analogues showed decreased nuclear localization of β-catenin and reduced mRNA expression of related antiapoptotic proteins. These data suggest inhibition of β-catenin nuclear translocation as a possible mode of action of the described cell-penetrating stapled peptides.
Collapse
Affiliation(s)
- Yuki Nagano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshimasa Kawaguchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
11
|
Mihara K, Nakajima N, Fujii I, Fujiwara D. Generation of inhibitory peptides for
IKKε
from a kinase‐focused phage library of helix‐loop‐helix peptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kousuke Mihara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Natsumi Nakajima
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| |
Collapse
|
12
|
Fujiwara D, Mihara K, Takayama R, Nakamura Y, Ueda M, Tsumuraya T, Fujii I. Chemical Modification of Phage-Displayed Helix-Loop-Helix Peptides to Construct Kinase-Focused Libraries. Chembiochem 2021; 22:3406-3409. [PMID: 34605137 PMCID: PMC9297947 DOI: 10.1002/cbic.202100450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Indexed: 11/11/2022]
Abstract
Conformationally constrained peptides hold promise as molecular tools in chemical biology and as a new modality in drug discovery. The construction and screening of a target‐focused library could be a promising approach for the generation of de novo ligands or inhibitors against target proteins. Here, we have prepared a protein kinase‐focused library by chemically modifying helix‐loop‐helix (HLH) peptides displayed on phage and subsequently tethered to adenosine. The library was screened against aurora kinase A (AurA). The selected HLH peptide Bip‐3 retained the α‐helical structure and bound to AurA with a KD value of 13.7 μM. Bip‐3 and the adenosine‐tethered peptide Bip‐3‐Adc provided IC50 values of 103 μM and 7.7 μM, respectively, suggesting that Bip‐3‐Adc bivalently inhibited AurA. In addition, the selectivity of Bip‐3‐Adc to several protein kinases was tested, and was highest against AurA. These results demonstrate that chemical modification can enable the construction of a kinase‐focused library of phage‐displayed HLH peptides.
Collapse
Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kousuke Mihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryo Takayama
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Yusuke Nakamura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Mitsuhiro Ueda
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Takeshi Tsumuraya
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| |
Collapse
|
13
|
Michigami M, Takahashi K, Yamashita H, Ye Z, Nakase I, Fujii I. A "ligand-targeting" peptide-drug conjugate: Targeted intracellular drug delivery by VEGF-binding helix-loop-helix peptides via receptor-mediated endocytosis. PLoS One 2021; 16:e0247045. [PMID: 33630870 PMCID: PMC7906330 DOI: 10.1371/journal.pone.0247045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/29/2021] [Indexed: 12/27/2022] Open
Abstract
As a new alternative to antibody-drug conjugates, we generated “ligand-targeting” peptide-drug conjugates (PDCs), which utilize receptor-mediated endocytosis for targeted intracellular drug delivery. The PDC makes a complex with an extracellular ligand and then binds to the receptor on the cell surface to stimulate intracellular uptake via the endocytic pathway. A helix-loop-helix (HLH) peptide was designed as the drug carrier and randomized to give a conformationally constrained peptide library. The phage-displayed library was screened against vascular endothelial growth factor (VEGF) to yield the binding peptide M49, which exhibited strong binding affinity (KD = 0.87 nM). The confocal fluorescence microscopy revealed that peptide M49 formed a ternary complex with VEGF and its receptor, which was then internalized into human umbilical vein endothelial cells (HUVECs) via VEGF receptor-mediated endocytosis. The backbone-cyclized peptide M49K was conjugated with a drug, monomethyl auristatin E, to afford a PDC, which inhibited VEGF-induced HUVEC proliferation. HLH peptides and their PDCs have great potential as a new modality for targeted molecular therapy.
Collapse
Affiliation(s)
- Masataka Michigami
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Kentaro Takahashi
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Haruna Yamashita
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | | | - Ikuhiko Nakase
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ikuo Fujii
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
- * E-mail:
| |
Collapse
|
14
|
González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
Collapse
Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
| | | | | |
Collapse
|
15
|
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.![]()
Collapse
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
| |
Collapse
|
16
|
Nadal‐Bufí F, Henriques ST. How to overcome endosomal entrapment of cell‐penetrating peptides to release the therapeutic potential of peptides? Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ferran Nadal‐Bufí
- School of Biomedical Sciences, Faculty of Health, Institute of Health & Biomedical Innovation, Queensland University of Technology Translational Research Institute Brisbane Queensland Australia
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Faculty of Health, Institute of Health & Biomedical Innovation, Queensland University of Technology Translational Research Institute Brisbane Queensland Australia
| |
Collapse
|
17
|
Sadek J, Wuo MG, Rooklin D, Hauenstein A, Hong SH, Gautam A, Wu H, Zhang Y, Cesarman E, Arora PS. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat Commun 2020; 11:1786. [PMID: 32286300 PMCID: PMC7156456 DOI: 10.1038/s41467-020-15576-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/12/2020] [Indexed: 01/07/2023] Open
Abstract
Protein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein. NF-κB signalling involves the scaffold protein NEMO, which can be bound by the oncoprotein vFLIP to promote cell survival and oncogenic transformation. Here the authors rationally engineer a tertiary protein mimic of NEMO to disrupt the vFLIP-NEMO interaction to induce cell death.
Collapse
Affiliation(s)
- Jouliana Sadek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Michael G Wuo
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - David Rooklin
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Arthur Hauenstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Archana Gautam
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, 10003, USA.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, 200122, Shanghai, China
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, 10003, USA.
| |
Collapse
|
18
|
Ramanayake Mudiyanselage TM, Michigami M, Ye Z, Uyeda A, Inoue N, Sugiura K, Fujii I, Fujiwara D. An Immune-Stimulatory Helix-Loop-Helix Peptide: Selective Inhibition of CTLA-4-B7 Interaction. ACS Chem Biol 2020; 15:360-368. [PMID: 31841301 DOI: 10.1021/acschembio.9b00743] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular-targeting peptides and mini-proteins are promising alternatives to antibodies in a wide range of applications in bioscience and medicine. We have developed a helix-loop-helix (HLH) peptide as an alternative to antibodies to inhibit specific protein interactions. Cytotoxic T lymphocyte antigen-4 (CTLA-4) downregulates immune responses of cytotoxic T-cells by interaction with B7-1, a co-stimulatory molecule expressed on antigen presenting cells (APCs). To induce immune stimulatory activity, we used directed evolution methods to generate a HLH peptide that binds to CTLA-4, inhibiting the CTLA-4-B7-1 interaction and inducing immune stimulatory activity. Yeast-displayed libraries of HLH peptides were constructed and screened against CTLA-4 and identified the binding peptide Y-2, which exhibits a moderate affinity. The affinity of Y-2 was improved by in vitro affinity maturation to afford a stronger binder, ERY2-4. Peptide ERY2-4 specifically bound to CTLA-4 with a KD of 196.8 ± 2.3 nM, comparable to the affinity of the CTLA-4-B7-1 interaction. Furthermore, ERY2-4 inhibited the CTLA-4-B7-1 interaction with an IC50 of 1.1 ± 0.03 μM and blocked the interaction between CTLA-4 and dendritic cells (DCs) presenting B7 on their surface. Importantly, ERY2-4 showed no cross-reactivity against CD28, suggesting it does not suppress T-cell activation. Finally, in a mixed lymphocyte reaction assay with DCs and T cells, ERY2-4 enhanced an allogeneic lymphocyte response. Since CTLA-4 is a critical immune checkpoint for restricting the cancer immune response, this inhibitory HLH peptide represents a new class of drug candidates for immunotherapy.
Collapse
Affiliation(s)
- Tharanga M.R. Ramanayake Mudiyanselage
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Zhengmao Ye
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norimitsu Inoue
- Department of Tumor Immunology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka-shi, Osaka 541-8567, Japan
| | - Kikuya Sugiura
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| |
Collapse
|
19
|
Lee HS, Postan M, Song A, Clark RJ, Bathgate RAD, Haugaard-Kedström LM, Rosengren KJ. Development of Relaxin-3 Agonists and Antagonists Based on Grafted Disulfide-Stabilized Scaffolds. Front Chem 2020; 8:87. [PMID: 32133341 PMCID: PMC7039932 DOI: 10.3389/fchem.2020.00087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
Relaxin-3 is a neuropeptide with important roles in metabolism, arousal, learning and memory. Its cognate receptor is the relaxin family peptide-3 (RXFP3) receptor. Relaxin-3 agonist and antagonist analogs have been shown to be able to modulate food intake in rodent models. The relaxin-3 B-chain is sufficient for receptor interactions, however, in the absence of a structural support, linear relaxin-3 B-chain analogs are rapidly degraded and thus unsuitable as drug leads. In this study, two different disulfide-stabilized scaffolds were used for grafting of important relaxin-3 B-chain residues to improve structure and stability. The use of both Veronica hederifolia Trypsin inhibitor (VhTI) and apamin grafting resulted in agonist and antagonist analogs with improved helicity. VhTI grafted peptides showed poor binding and low potency at RXFP3, on the other hand, apamin variants retained significant activity. These variants also showed improved half-life in serum from ~5 min to >6 h, and thus are promising RXFP3 specific pharmacological tools and drug leads for neuropharmacological diseases.
Collapse
Affiliation(s)
- Han Siean Lee
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Postan
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Angela Song
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Richard J Clark
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ross A D Bathgate
- Florey Department of Neuroscience and Mental Health, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Linda M Haugaard-Kedström
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - K Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
20
|
Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
Collapse
|
21
|
Giachino C, Viale M, Vecchio G. Exploring the Functionalization of Polymeric Nanoparticles Based on Cyclodextrins for Tumor Cell Targeting. ChemistrySelect 2019. [DOI: 10.1002/slct.201903774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carmela Giachino
- Dipartimento di Scienze ChimichetUniversità degli Studi di Catania Viale A. Doria 6 95125 Catania Italy
| | - Maurizio Viale
- U.O.C. BioterapieOspedale Policlinico San Martino L.go R. Benzi 10 16132 Genova Italy
| | - Graziella Vecchio
- Dipartimento di Scienze ChimichetUniversità degli Studi di Catania Viale A. Doria 6 95125 Catania Italy
| |
Collapse
|
22
|
Philippe GJB, Gaspar D, Sheng C, Huang YH, Benfield AH, Condon ND, Weidmann J, Lawrence N, Löwer A, Castanho MARB, Craik DJ, Troeira Henriques S. Cell Membrane Composition Drives Selectivity and Toxicity of Designed Cyclic Helix-Loop-Helix Peptides with Cell Penetrating and Tumor Suppressor Properties. ACS Chem Biol 2019; 14:2071-2087. [PMID: 31390185 DOI: 10.1021/acschembio.9b00593] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The tumor suppressor protein p53 is inactive in a large number of cancers, including some forms of sarcoma, breast cancer, and leukemia, due to overexpression of its intrinsic inhibitors MDM2 and MDMX. Reactivation of p53 tumor suppressor activity, via disruption of interactions between MDM2/X and p53 in the cytosol, is a promising strategy to treat cancer. Peptides able to bind MDM2 and/or MDMX were shown to prevent MDM2/X:p53 interactions, but most possess low cell penetrability, low stability, and/or high toxicity to healthy cells. Recently, the designed peptide cHLH-p53-R was reported to possess high affinity for MDM2, resistance toward proteases, cell-penetrating properties, and toxicity toward cancer cells. This peptide uses a stable cyclic helix-loop-helix (cHLH) scaffold, which includes two helices connected with a Gly loop and cyclized to improve stability. In the current study, we were interested in examining the cell selectivity of cHLH-p53-R, its cellular internalization, and ability to reactivate the p53 pathway. We designed analogues of cHLH-p53-R and employed biochemical and biophysical methodologies using in vitro model membranes and cell-based assays to compare their structure, activity, and mode-of-action. Our studies show that cHLH is an excellent scaffold to stabilize and constrain p53-mimetic peptides with helical conformation, and reveal that anticancer properties of cHLH-p53-R are mediated by its ability to selectively target, cross, and disrupt cancer cell membranes, and not by activation of the p53 pathway. These findings highlight the importance of examining the mode-of-action of designed peptides to fully exploit their potential to develop targeted therapies.
Collapse
Affiliation(s)
- Grégoire J.-B. Philippe
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Diana Gaspar
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Caibin Sheng
- Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Aurélie H. Benfield
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Miguel A. R. B. Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - David J. Craik
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| |
Collapse
|
23
|
Bosma T, Rink R, Moosmeier MA, Moll GN. Genetically Encoded Libraries of Constrained Peptides. Chembiochem 2019; 20:1754-1758. [PMID: 30794341 DOI: 10.1002/cbic.201900031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Indexed: 02/01/2023]
Abstract
Many therapeutic peptides can still be improved with respect to target specificity, target affinity, resistance to peptidases/proteases, physical stability, and capacity to pass through membranes required for oral delivery. Several modifications can improve the peptides' properties, in particular those that impose (a) conformational constraint(s). Screening of constrained peptides and the identification of hits is greatly facilitated by the generation of genetically encoded libraries. Recent breakthrough bacterial, phage, and yeast display screening systems of ribosomally synthesized post-translationally constrained peptides, particularly those of lanthipeptides, are earning special attention. Here we provide an overview of display systems for constrained, genetically encoded peptides and indicate prospects of constrained peptide-displaying phage and bacterial systems as such in vivo.
Collapse
Affiliation(s)
- Tjibbe Bosma
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | - Rick Rink
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | | | - Gert N Moll
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| |
Collapse
|
24
|
Zhang L, Sheng Y, Zehtab Yazdi A, Sarikhani K, Wang F, Jiang Y, Liu J, Zheng T, Wang W, Ouyang P, Chen P. Surface-assisted assembly of a histidine-rich lipidated peptide for simultaneous exfoliation of graphite and functionalization of graphene nanosheets. NANOSCALE 2019; 11:2999-3012. [PMID: 30698183 DOI: 10.1039/c8nr08397e] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biological molecules have promising potential to exfoliate graphite and produce biocompatible graphene nano-materials for biomedical applications. Here, a systematic design of a histidine-rich lipidated peptide sequence is presented that simultaneously exfoliates graphite flakes and functionalizes the resulting graphene nanosheets (∼150 nm lateral size) with long-term dispersion stability in aqueous solution (>8 months). The details of peptide/peptide and peptide/graphite interactions are probed using various microscopy, spectroscopy and molecular dynamics simulation methods. The results show that histidine and stearic acid interact with the graphite surface through π-π stacking and hydrophobic forces, respectively. Surface-assisted assembly of peptide molecules is then initiated via hydrogen bonds between deprotonated histidine segments, and a textured peptide nano-structure is formed. The work of adhesion between the peptide and graphite is found to be high enough to promote exfoliation of graphite flakes through layer-by-layer peeling of graphene nanosheets. The positively charged arginine in the peptide is exposed outward, and is responsible for the stable dispersion. The peptide molecules are sufficiently small, presenting the possibility to insert into and increase the spacing between the graphitic layers for enhanced exfoliation. The peptide-functionalized graphene nanosheets not only show great biocompatibility with cells in vitro, but also enhance cancer drug uptake by the cells.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, CanadaN2L 3G1.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
He W, Yan J, Sui F, Wang S, Su X, Qu Y, Yang Q, Guo H, Ji M, Lu W, Shao Y, Hou P. Turning a Luffa Protein into a Self-Assembled Biodegradable Nanoplatform for Multitargeted Cancer Therapy. ACS NANO 2018; 12:11664-11677. [PMID: 30335959 DOI: 10.1021/acsnano.8b07079] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The peptide-derived self-assembly platform has attracted increasing attention for its great potential to develop into multitargeting nanomedicines as well as its inherent biocompatibility and biodegradability. However, their clinical application potentials are often compromised by low stability, weak membrane penetrating ability, and limited functions. Herein, inspired by a natural protein from the seeds of Luffa cylindrica, we engineered via epitope grafting and structure design a hybrid peptide-based nanoplatform, termed Lupbin, which is capable of self-assembling into a stable superstructure and concurrently targeting multiple protein-protein interactions (PPIs) located in cytoplasm and nuclei. We showed that Lupbin can efficiently penetrate cell membrane, escape from early endosome-dependent degradation, and subsequently disassemble into free monomers with wide distribution in cytosol and nucleus. Importantly, Lupbin abrogated tumor growth and metastasis through concurrent blockade of the Wnt/β-catenin signaling and reactivation of the p53 signaling, with a highly favorable in vivo biosafety profile. Our strategy expands the application of self-assembled nanomedicines into targeting intercellular PPIs, provides a potential nanoplatform with high stability for multitargeted cancer therapy, and likely reinvigorates the development of peptide-based therapeutics for the treatment of different human diseases including cancer.
Collapse
Affiliation(s)
- Wangxiao He
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , China
| | - Jin Yan
- Frontier Institute of Science and Technology, State Key Laboratory for Mechanical Behavior of Materials , Xi'an Jiaotong University , Xi'an 710049 , China
| | - Fang Sui
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| | - Simeng Wang
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| | - Xi Su
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| | - Yiping Qu
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| | - Qingchen Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , China
| | - Hui Guo
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| | - Meiju Ji
- Center for Translational Medicine , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| | - Wuyuan Lu
- Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| | - Yongping Shao
- Frontier Institute of Science and Technology, Center for Translational Medicine, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , China
| | - Peng Hou
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province and Department of Endocrinology , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an 710061 , China
| |
Collapse
|
26
|
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: 96] [Impact Index Per Article: 16.0] [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.
Collapse
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
| |
Collapse
|
27
|
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
| |
Collapse
|
28
|
Meuleman TJ, Dunlop JI, Owsianka AM, van de Langemheen H, Patel AH, Liskamp RMJ. Immobilization by Surface Conjugation of Cyclic Peptides for Effective Mimicry of the HCV-Envelope E2 Protein as a Strategy toward Synthetic Vaccines. Bioconjug Chem 2018; 29:1091-1101. [PMID: 29382188 DOI: 10.1021/acs.bioconjchem.7b00755] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mimicry of the binding interface of antibody-antigen interactions using peptide-based modulators (i.e., epitope mimics) has promising applications for vaccine design. These epitope mimics can be synthesized in a streamlined and straightforward fashion, thereby allowing for high-throughput analysis. The design of epitope mimics is highly influenced by their spatial configuration and structural conformation. It is widely assumed that for proper mimicry sufficient conformational constraints have to be implemented. This paper describes the synthesis of bromide derivatives functionalized with a flexible TEG linker equipped with a thiol-moiety that could be used to support cyclic or linear peptides. The cyclic and linear epitope mimics were covalently conjugated via the free thiol-moiety on maleimide-activated plate surfaces. The resulting covalent, uniform, and oriented coated surface of cyclic or linear epitope mimics were subjected to an ELISA to investigate the effect of peptide cyclization with respect to mimicry of an antigen-antibody interaction of the HCV E2 glycoprotein. To the best of our knowledge, the benefit of cyclized peptides over linear peptides has been clearly demonstrated here for the first time. Cyclic epitope mimics, and not the linear epitope mimics, demonstrated specificity toward their monoclonal antibodies HC84.1 and V3.2, respectively. The described strategy for the construction of epitope mimics shows potential for high-throughput screening of key binding residues by simply changing the amino acid sequences within synthetic peptides. In this way, leucine-438 has been identified as a key binding residue for binding monoclonal antibody V3.2.
Collapse
Affiliation(s)
- Theodorus J Meuleman
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , United Kingdom
| | - James I Dunlop
- MRC-University of Glasgow Centre for Virus Research , Garscube Campus, Sir Michael Stoker Building, 464 Bearsden Road , Glasgow G61 1QH , United Kingdom
| | - Anna M Owsianka
- MRC-University of Glasgow Centre for Virus Research , Garscube Campus, Sir Michael Stoker Building, 464 Bearsden Road , Glasgow G61 1QH , United Kingdom
| | - Helmus van de Langemheen
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , United Kingdom
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research , Garscube Campus, Sir Michael Stoker Building, 464 Bearsden Road , Glasgow G61 1QH , United Kingdom
| | - Rob M J Liskamp
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , United Kingdom
| |
Collapse
|
29
|
Automated Single-Cell Analysis and Isolation System: A Paradigm Shift in Cell Screening Methods for Bio-medicines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:7-17. [DOI: 10.1007/978-981-13-0502-3_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
30
|
Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
Collapse
Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
31
|
van de Langemheen H, Korotkovs V, Bijl J, Wilson C, Kale SS, Heinis C, Liskamp RMJ. Polar Hinges as Functionalized Conformational Constraints in (Bi)cyclic Peptides. Chembiochem 2017; 18:387-395. [DOI: 10.1002/cbic.201600612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Helmus van de Langemheen
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Valerijs Korotkovs
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Joachim Bijl
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Claire Wilson
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Sangram S. Kale
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Rob M. J. Liskamp
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| |
Collapse
|