1
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Santini BL, Wendel S, Halbwedl N, Knipp A, Zacharias M. cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery. Comput Struct Biotechnol J 2024; 23:3155-3162. [PMID: 39253058 PMCID: PMC11381751 DOI: 10.1016/j.csbj.2024.08.008] [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] [Received: 06/26/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 09/11/2024] Open
Abstract
Cyclic peptides have emerged as versatile scaffolds in drug discovery due to their stability and specificity. Here, we present the cPEPmatch webserver (accessible at https://t38webservices.nat.tum.de/cpepmatch/), an easy-to-use interface for the rational design of cyclic peptides targeting protein-protein interactions combined with a semi-quantitative evaluation of binding stability. This platform also offers access to a comprehensive database of cyclic peptide crystal structures. We demonstrate the webserver's utility through a series of case studies involving medically relevant protein systems, highlighting its potential to significantly advance drug discovery efforts.
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Affiliation(s)
- Brianda L Santini
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Stephanie Wendel
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Niklas Halbwedl
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Asha Knipp
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
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2
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Taya T, Kami D, Teruyama F, Matoba S, Gojo S. Peptide-encoding gene transfer to modulate intracellular protein-protein interactions. Mol Ther Methods Clin Dev 2024; 32:101226. [PMID: 38516692 PMCID: PMC10952081 DOI: 10.1016/j.omtm.2024.101226] [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] [Received: 09/25/2023] [Accepted: 02/24/2024] [Indexed: 03/23/2024]
Abstract
Peptide drug discovery has great potential, but the cell membrane is a major obstacle when the target is an intracellular protein-protein interaction (PPI). It is difficult to target PPIs with small molecules; indeed, there are no intervention tools that can target any intracellular PPI. In this study, we developed a platform that enables the introduction of peptides into cells via mRNA-based gene delivery. Peptide-length nucleic acids do not enable stable ribosome binding and exhibit little to no translation into protein. In this study, a construct was created in which the sequence encoding dihydrofolate reductase (DHFR) was placed in front of the sequence encoding the target peptide, together with a translation skipping sequence, as a sequence that meets the requirements of promoting ribosome binding and rapid decay of the translated protein. This enabled efficient translation from the mRNA encoding the target protein while preventing unnecessary protein residues. Using this construct, we showed that it can inhibit Drp1/Fis1 binding, one of the intracellular PPIs, which governs mitochondrial fission, an important aspect of mitochondrial dynamics. In addition, it was shown to inhibit pathological hyperfission, normalize mitochondrial dynamics and metabolism, and inhibit apoptosis of the mitochondrial pathway.
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Affiliation(s)
- Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Fumiya Teruyama
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Pharmacology Research Department, Tokyo New Drug Research Laboratories, Kowa Company, Ltd, Tokyo, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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3
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Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [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: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
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Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
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4
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Ferrie RP, Fuselier T, Wimley WC. Cytosolic Delivery of Bioactive Cyclic Peptide Cargo by Spontaneous Membrane Translocating Peptides. ACS OMEGA 2024; 9:8179-8187. [PMID: 38405535 PMCID: PMC10882622 DOI: 10.1021/acsomega.3c08701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/23/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Cyclic peptides that inhibit protein-protein interactions have significant advantages over linear peptides and small molecules for modulating cellular signaling networks in cancer and other diseases. However, the permeability barrier of the plasma membrane remains a formidable obstacle to the development of cyclic peptides into applicable drugs. Here, we test the ability of a family of synthetically evolved spontaneous membrane translocating peptides (SMTPs) to deliver phalloidin, a representative bioactive cyclic peptide, to the cytosol of human cells in culture. Phalloidin does not enter cells spontaneously, but if delivered to the cytosol, it inhibits actin depolymerization. We thus use a wound-healing cell mobility assay to assess the biological activity of phalloidin conjugated to three SMTPs that we previously discovered. All three SMTPs can deliver phalloidin to the cell cytosol, and one does so at concentrations as low as 3 μM. Delivery occurs despite the fact that the SMTPs were originally selected based on membrane translocation with no cargo other than a small fluorescent dye. These results show that SMTPs are viable delivery vehicles for cyclic peptides, although their efficiency is moderate. Further, these results suggest that one additional generation of synthetic molecular evolution could be used to optimize SMTPs for the efficient delivery of any bioactive cyclic peptide into cells.
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Affiliation(s)
- Ryan P. Ferrie
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
| | - Taylor Fuselier
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
| | - William C. Wimley
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
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5
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Abdel-Rahman SA, Santini BL, Calvo-Barreiro L, Zacharias M, Gabr M. Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction. Bioorg Med Chem Lett 2024; 99:129599. [PMID: 38185345 DOI: 10.1016/j.bmcl.2024.129599] [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: 11/08/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
Compared to small molecules and antibodies, cyclic peptides exhibit unique biochemical and therapeutic attributes in the realm of pharmaceutical applications. The interaction between the inducible costimulator (ICOS) and its ligand (ICOSL) plays a key role in T-cell differentiation and activation. ICOS/ICOSL inhibition results in a reduction in the promotion of immunosuppressive regulatory T cells (Tregs) in both hematologic malignancies and solid tumors. Herein, we implement the computational cPEPmatch approach to design the first examples of cyclic peptides that inhibit ICOS/ICOSL interaction. The top cyclic peptide from our approach possessed an IC50 value of 1.87 ± 0.15 μM as an ICOS/ICOSL inhibitor and exhibited excellent in vitro pharmacokinetic properties as a drug candidate. Our work will lay the groundwork for future endeavors in cancer drug discovery, with the goal of developing cyclic peptides that target the ICOS/ICOSL interaction.
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Affiliation(s)
- Somaya A Abdel-Rahman
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Brianda L Santini
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Laura Calvo-Barreiro
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY 10065, USA
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Moustafa Gabr
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY 10065, USA.
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6
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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.
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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
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7
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Ohta A, Tanada M, Shinohara S, Morita Y, Nakano K, Yamagishi Y, Takano R, Kariyuki S, Iida T, Matsuo A, Ozeki K, Emura T, Sakurai Y, Takano K, Higashida A, Kojima M, Muraoka T, Takeyama R, Kato T, Kimura K, Ogawa K, Ohara K, Tanaka S, Kikuchi Y, Hisada N, Hayashi R, Nishimura Y, Nomura K, Tachibana T, Irie M, Kawada H, Torizawa T, Murao N, Kotake T, Tanaka M, Ishikawa S, Miyake T, Tamiya M, Arai M, Chiyoda A, Akai S, Sase H, Kuramoto S, Ito T, Shiraishi T, Kojima T, Iikura H. Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. J Am Chem Soc 2023; 145:24035-24051. [PMID: 37874670 DOI: 10.1021/jacs.3c07145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Establishing a technological platform for creating clinical compounds inhibiting intracellular protein-protein interactions (PPIs) can open the door to many valuable drugs. Although small molecules and antibodies are mainstream modalities, they are not suitable for a target protein that lacks a deep cavity for a small molecule to bind or a protein found in intracellular space out of an antibody's reach. One possible approach to access these targets is to utilize so-called middle-size cyclic peptides (defined here as those with a molecular weight of 1000-2000 g/mol). In this study, we validated a new methodology to create oral drugs beyond the rule of 5 for intracellular tough targets by elucidating structural features and physicochemical properties for drug-like cyclic peptides and developing library technologies to afford highly N-alkylated cyclic peptide hits. We discovered a KRAS inhibitory clinical compound (LUNA18) as the first example of our platform technology.
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Affiliation(s)
- Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shojiro Shinohara
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kazuhiko Nakano
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yusuke Yamagishi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Ryusuke Takano
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shiori Kariyuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takeo Iida
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kazuhisa Ozeki
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takashi Emura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yuuji Sakurai
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Atsuko Higashida
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Miki Kojima
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Terushige Muraoka
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tatsuya Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kaori Kimura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kotaro Ogawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shota Tanaka
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yasufumi Kikuchi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Nozomi Hisada
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tatsuhiko Tachibana
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takuya Torizawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Naoaki Murao
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Masahiko Tanaka
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Taiji Miyake
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Masako Arai
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Sho Akai
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Tetsuo Kojima
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan
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8
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Mizuno-Kaneko M, Hashimoto I, Miyahara K, Kochi M, Ohashi N, Tsumura K, Suzuki K, Tamura T. Molecular Design of Cyclic Peptides with Cell Membrane Permeability and Development of MDMX-p53 Inhibitor. ACS Med Chem Lett 2023; 14:1174-1178. [PMID: 37736191 PMCID: PMC10510666 DOI: 10.1021/acsmedchemlett.3c00102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023] Open
Abstract
Cyclic peptides have been expected to be one of the modalities of intracellular protein-protein interaction (PPI) inhibitors, but they are generally known to have low cell membrane permeability. In this study, we focused on the conformation of cyclic peptides in the cell membrane to determine the requirement for their cell membrane permeability through passive diffusion. Utilizing the requirement, we searched for structures with high affinity for MDMX via computational chemistry and acquired cyclic peptide 19 (Papp = 0.80 × 10-6 cm s-1, IC50 = 0.07 μM).
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Affiliation(s)
- Mai Mizuno-Kaneko
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Ichihiko Hashimoto
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kenta Miyahara
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Masahiro Kochi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Noriyuki Ohashi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kyosuke Tsumura
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Koo Suzuki
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Takashi Tamura
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
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9
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Pepanian A, Binbay FA, Roy S, Nubbemeyer B, Koley A, Rhodes CA, Ammer H, Pei D, Ghosh P, Imhof D. Bicyclic Peptide Library Screening for the Identification of Gαi Protein Modulators. J Med Chem 2023; 66:12396-12406. [PMID: 37587416 PMCID: PMC11000586 DOI: 10.1021/acs.jmedchem.3c00873] [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: 08/18/2023]
Abstract
Noncanonical G protein activation and inactivation, particularly for the Gαi/s protein subfamilies, have long been a focus of chemical research. Combinatorial libraries were already effectively applied to identify modulators of the guanine-nucleotide exchange, as can be exemplified with peptides such as KB-752 and GPM-1c/d, the so-called guanine-nucleotide exchange modulators. In this study, we identified novel bicyclic peptides from a combinatorial library screening that show prominent properties as molecular switch-on/off modulators of Gαi signaling. Among the series of hits, the exceptional paradigm of GPM-3, a protein and state-specific bicyclic peptide, is the first chemically identified GAP (GTPase-activating protein) modulator with a high binding affinity for Gαi protein. Computational analyses identified and assessed the structure of the bicyclic peptides, novel ligand-protein interaction sites, and their subsequent impact on the nucleotide binding site. This approach can therefore lead the way for the development of efficient chemical biological probes targeting Gαi protein modulation within a cellular context.
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Affiliation(s)
- Anna Pepanian
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Furkan Ayberk Binbay
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Suchismita Roy
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Britta Nubbemeyer
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Hermann Ammer
- Institute of Pharmacology Toxicology and Pharmacy, Veterinary Faculty, Ludwig Maximilian University of Munich, Königinstr. 16, 80539 Munich, Germany
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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10
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Kasper SH, Otten S, Squadroni B, Orr‐Terry C, Kuang Y, Mussallem L, Ge L, Yan L, Kannan S, Verma CS, Brown CJ, Johannes CW, Lane DP, Chandramohan A, Partridge AW, Roberts LR, Josien H, Therien AG, Hett EC, Howell BJ, Peier A, Ai X, Cassaday J. A high-throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell-based assays. Bioeng Transl Med 2023; 8:e10542. [PMID: 37693049 PMCID: PMC10487316 DOI: 10.1002/btm2.10542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 09/12/2023] Open
Abstract
Cyclic peptides are poised to target historically difficult to drug intracellular protein-protein interactions, however, their general cell impermeability poses a challenge for characterizing function. Recent advances in microfluidics have enabled permeabilization of the cytoplasmic membrane by physical cell deformation (i.e., mechanoporation), resulting in intracellular delivery of impermeable macromolecules in vector- and electrophoretic-free approaches. However, the number of payloads (e.g., peptides) and/or concentrations delivered via microfluidic mechanoporation is limited by having to pre-mix cells and payloads, a manually intensive process. In this work, we show that cells are momentarily permeable (t 1/2 = 1.1-2.8 min) after microfluidic vortex shedding (μVS) and that lower molecular weight macromolecules can be cytosolically delivered upon immediate exposure after cells are processed/permeabilized. To increase the ability to screen peptides, we built a system, dispensing-microfluidic vortex shedding (DμVS), that integrates a μVS chip with inline microplate-based dispensing. To do so, we synced an electronic pressure regulator, flow sensor, on/off dispense valve, and an x-y motion platform in a software-driven feedback loop. Using this system, we were able to deliver low microliter-scale volumes of transiently mechanoporated cells to hundreds of wells on microtiter plates in just several minutes (e.g., 96-well plate filled in <2.5 min). We validated the delivery of an impermeable peptide directed at MDM2, a negative regulator of the tumor suppressor p53, using a click chemistry- and NanoBRET-based cell permeability assay in 96-well format, with robust delivery across the full plate. Furthermore, we demonstrated that DμVS could be used to identify functional, low micromolar, cellular activity of otherwise cell-inactive MDM2-binding peptides using a p53 reporter cell assay in 96- and 384-well format. Overall, DμVS can be combined with downstream cell assays to investigate intracellular target engagement in a high-throughput manner, both for improving structure-activity relationship efforts and for early proof-of-biology of non-optimized peptide (or potentially other macromolecular) tools.
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Affiliation(s)
| | | | | | | | - Yi Kuang
- Merck & Co., Inc.CambridgeMassachusettsUSA
| | | | - Lan Ge
- Merck & Co., Inc.KenilworthNew JerseyUSA
| | - Lin Yan
- Merck & Co., Inc.KenilworthNew JerseyUSA
| | | | - Chandra S. Verma
- Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | | | | | - David P. Lane
- Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | | | | | | | | | | | | | | | | | - Xi Ai
- Merck & Co., Inc.KenilworthNew JerseyUSA
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11
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Mendoza A, Bernardino SJ, Dweck MJ, Valencia I, Evans D, Tian H, Lee W, Li Y, Houk KN, Harran PG. Cascade Synthesis of Fluorinated Spiroheterocyclic Scaffolding for Peptidic Macrobicycles. J Am Chem Soc 2023. [PMID: 37441722 DOI: 10.1021/jacs.3c03071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Octafluorocyclopentene (OFCP) engages linear, unprotected peptides in polysubstitution cascades that generate complex fluorinated polycycles. The reactions occur in a single flask at 0-25 °C and require no catalysts or heavy metals. OFCP can directly polycyclize linear sequences using native functionality, or fluorospiroheterocyclic intermediates can be intercepted with exogenous nucleophiles. The latter tactic generates molecular hybrids composed of peptides, sugars, lipids, and heterocyclic components. The platform can create stereoisomers of both single- and double-looped macrocycles. Calculations indicate that the latter can mimic diverse protein surface loops. Subsets of the molecules have low energy conformers that shield the polar surface area through intramolecular hydrogen bonding. A significant fraction of OFCP-derived macrocycles tested show moderate to high passive permeability in parallel artificial membrane permeability assays.
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Affiliation(s)
- Angel Mendoza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Salvador J Bernardino
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Morris J Dweck
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Isabel Valencia
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Haowen Tian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - William Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yu Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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12
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Franco HEO, Le AV, Chang NY, Hartman MCT. p-Chloropropynyl Phenylalanine, a Versatile Non-Canonical Amino Acid for Co-Translational Peptide Macrocyclization and Side Chain Diversification. Chembiochem 2023; 24:e202300020. [PMID: 37156744 PMCID: PMC11165969 DOI: 10.1002/cbic.202300020] [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: 01/11/2023] [Revised: 04/07/2023] [Indexed: 05/10/2023]
Abstract
Macrocyclization has proven to be a beneficial strategy to improve upon some of the disadvantages of peptides as therapeutics. Nevertheless, many peptide cyclization strategies are not compatible with in vitro display technologies like mRNA display. Here we describe the novel amino acid p-chloropropynyl phenylalanine (pCPF). pCPF is a substrate for a mutant phenylalanyl-tRNA synthetase and its introduction into peptides via in vitro translation leads to spontaneous peptide macrocyclization in the presence of peptides containing cysteine. Macrocyclization occurs efficiently with a wide variety of ring sizes. Moreover, pCPF can be reacted with thiols after charging onto tRNA, enabling the testing of diverse ncAAs in translation. The versatility of pCPF should facilitate downstream studies of translation and enable the creation of novel macrocyclic peptide libraries.
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Affiliation(s)
- H. Estheban Osorio Franco
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
| | - Anthony V. Le
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
| | - Nathan Y. Chang
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
| | - Matthew C. T. Hartman
- Chemistry, Virginia Commonwealth University, 1001 W Main St, Richmond, 23284, VA
- Massey Cancer Center, Virginia Commonwealth University
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13
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Chen SY, Zacharias M. What Makes a Good Protein-Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism. ACS CENTRAL SCIENCE 2023; 9:969-979. [PMID: 37252344 PMCID: PMC10214505 DOI: 10.1021/acscentsci.3c00003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Indexed: 05/31/2023]
Abstract
Protein-protein interactions (PPIs) are essential for biological processes including immune reactions and diseases. Inhibition of PPIs by drug-like compounds is a common basis for therapeutic approaches. In many cases the flat interface of PP complexes prevents discovery of specific compound binding to cavities on one partner and PPI inhibition. However, frequently new pockets are formed at the PP interface that allow accommodation of stabilizers which is often as desirable as inhibition but a much less explored alternative strategy. Herein, we employ molecular dynamics simulations and pocket detection to investigate 18 known stabilizers and associated PP complexes. For most cases, we find that a dual-binding mechanism, a similar stabilizer interaction strength with each protein partner, is an important prerequisite for effective stabilization. A few stabilizers follow an allosteric mechanism by stabilizing the protein bound structure and/or increase the PPI indirectly. On 226 protein-protein complexes, we find in >75% of the cases interface cavities suitable for binding of drug-like compounds. We propose a computational compound identification workflow that exploits new PP interface cavities and optimizes the dual-binding mechanism and apply it to 5 PP complexes. Our study demonstrates a great potential for in silico PPI stabilizers discovery with a wide range of therapeutic applications.
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14
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Shanker S, Sanner MF. Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking. J Chem Inf Model 2023; 63:3158-3170. [PMID: 37167566 DOI: 10.1021/acs.jcim.3c00602] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide interactions and shown to significantly outperform RoseTTAfold as well as a conventional blind docking method: PIPER-FlexPepDock. Since then, new AlphaFold2 models, trained specifically to predict multimeric assemblies, have been released and a new ab initio folding model OmegaFold has become available. Here, we assess docking success rates for these new DL folding models and compare their performance with our state-of-the-art, focused peptide-docking software AutoDock CrankPep (ADCP). The evaluation is done using the same dataset and performance metric for all methods. We show that, for a set of 99 nonredundant protein-peptide complexes, the new AlphaFold2 model outperforms other Deep Learning approaches and achieves remarkable docking success rates for peptides. While the docking success rate of ADCP is more modest when considering the top-ranking solution only, it samples correct solutions for around 62% of the complexes. Interestingly, different methods succeed on different complexes, and we describe a consensus docking approach using ADCP and AlphaFold2, which achieves a remarkable 60% for the top-ranking results and 66% for the top 5 results for this set of 99 protein-peptide complexes.
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Affiliation(s)
- Sudhanshu Shanker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michel F Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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15
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Moxam J, Naylon S, Richaud AD, Zhao G, Padilla A, Roche SP. Passive Membrane Permeability of Sizable Acyclic β-Hairpin Peptides. ACS Med Chem Lett 2023; 14:278-284. [PMID: 36923919 PMCID: PMC10009788 DOI: 10.1021/acsmedchemlett.2c00486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The recent shift toward increasingly larger drug modalities has created a significant demand for novel classes of compounds with high membrane permeability that can inhibit intracellular protein-protein interactions (PPIs). While major advances have been made in the design of cell-permeable helices, stapled β-sheets, and cyclic peptides, the development of large acyclic β-hairpins lags far behind. Therefore, we investigated a series of 26 β-hairpins (MW > 1.6 kDa) belonging to a chemical space far beyond the Lipinski "rule of five" (fbRo5) and showed that, in addition to their innate plasticity, the lipophilicity of these peptides (log D 7.4 ≈ 0 ± 0.7) can be tuned to drastically improve the balance between aqueous solubility and passive membrane permeability.
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Affiliation(s)
- Jillene Moxam
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Sarah Naylon
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alexis D. Richaud
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alberto Padilla
- Department
of Natural Science, Keiser University, Fort Lauderdale, Florida 33309, United States
| | - Stéphane P. Roche
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
- Center
for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
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16
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O'Brien Laramy MN, Luthra S, Brown MF, Bartlett DW. Delivering on the promise of protein degraders. Nat Rev Drug Discov 2023; 22:410-427. [PMID: 36810917 DOI: 10.1038/s41573-023-00652-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/23/2023]
Abstract
Over the past 3 years, the first bivalent protein degraders intentionally designed for targeted protein degradation (TPD) have advanced to clinical trials, with an initial focus on established targets. Most of these clinical candidates are designed for oral administration, and many discovery efforts appear to be similarly focused. As we look towards the future, we propose that an oral-centric discovery paradigm will overly constrain the chemical designs that are considered and limit the potential to drug novel targets. In this Perspective, we summarize the current state of the bivalent degrader modality and propose three categories of degrader designs, based on their likely route of administration and requirement for drug delivery technologies. We then describe a vision for how parenteral drug delivery, implemented early in research and supported by pharmacokinetic-pharmacodynamic modelling, can enable exploration of a broader drug design space, expand the scope of accessible targets and deliver on the promise of protein degraders as a therapeutic modality.
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Affiliation(s)
| | - Suman Luthra
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, MA, USA
| | - Matthew F Brown
- Discovery Sciences, Worldwide Research, Development, and Medical, Pfizer Inc., Groton, CT, USA
| | - Derek W Bartlett
- Pharmacokinetics, Dynamics, & Metabolism, Worldwide Research, Development, and Medical, Pfizer Inc., San Diego, CA, USA
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17
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Functional Peptides from One-bead One-compound High-throughput Screening Technique. Chem Res Chin Univ 2023. [DOI: 10.1007/s40242-023-2356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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18
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Li K, Tokareva OS, Thomson TM, Wahl SCT, Travaline TL, Ramirez JD, Choudary SK, Agarwal S, Walkup WG, Olsen TJ, Brennan MJ, Verdine GL, McGee JH. De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries. Proc Natl Acad Sci U S A 2022; 119:e2210435119. [PMID: 36534810 PMCID: PMC9907135 DOI: 10.1073/pnas.2210435119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
The α-helix is one of the most common protein surface recognition motifs found in nature, and its unique amide-cloaking properties also enable α-helical polypeptide motifs to exist in membranes. Together, these properties have inspired the development of α-helically constrained (Helicon) therapeutics that can enter cells and bind targets that have been considered "undruggable", such as protein-protein interactions. To date, no general method for discovering α-helical binders to proteins has been reported, limiting Helicon drug discovery to only those proteins with previously characterized α-helix recognition sites, and restricting the starting chemical matter to those known α-helical binders. Here, we report a general and rapid screening method to empirically map the α-helix binding sites on a broad range of target proteins in parallel using large, unbiased Helicon phage display libraries and next-generation sequencing. We apply this method to screen six structurally diverse protein domains, only one of which had been previously reported to bind isolated α-helical peptides, discovering 20 families that collectively comprise several hundred individual Helicons. Analysis of 14 X-ray cocrystal structures reveals at least nine distinct α-helix recognition sites across these six proteins, and biochemical and biophysical studies show that these Helicons can block protein-protein interactions, inhibit enzymatic activity, induce conformational rearrangements, and cause protein dimerization. We anticipate that this method will prove broadly useful for the study of protein recognition and for the development of both biochemical tools and therapeutics for traditionally challenging protein targets.
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Affiliation(s)
- Kunhua Li
- FOG Pharmaceuticals Inc., Cambridge, MA02140
| | | | | | | | | | | | | | | | | | | | | | - Gregory L. Verdine
- FOG Pharmaceuticals Inc., Cambridge, MA02140
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
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19
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Krzyzanowski A, Esser LM, Willaume A, Prudent R, Peter C, ‘t Hart P, Waldmann H. Development of Macrocyclic PRMT5-Adaptor Protein Interaction Inhibitors. J Med Chem 2022; 65:15300-15311. [PMID: 36378254 PMCID: PMC9706563 DOI: 10.1021/acs.jmedchem.2c01273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The PRMT5-MEP50 methyltransferase is a major target for anticancer drug discovery, and modulators of its interactions with different regulatory proteins are in high demand because they modulate PRMT5 substrate selectivity. We describe a strategy for the development of a PRMT5/adaptor protein PPI inhibitor, which includes the design and synthesis of macrocyclic peptides based on the motif for the interaction of PRMT5 with its adaptor protein RioK1. After the initial exploration of different macrocycle sizes and cyclization linkages, analysis of a peptide library identified hot spots for the variation of the amino acid structure. The incorporation of nonproteinogenic amino acids into the macrocyclic peptide led to a potent cyclic PRMT5 binding peptide (Ki = 66 nM), which selectively inhibits the interaction of PRMT5 with the adaptor proteins RioK1 and pICln (IC50 = 654 nM) but not with the alternative adaptor protein MEP50. The inhibitor is a promising tool for further biological investigation of this intriguing protein interface.
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Affiliation(s)
- Adrian Krzyzanowski
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany,Faculty
of Chemistry, Chemical Biology, Technical
University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| | - Lea Marie Esser
- Institute
of Molecular Medicine I, Medical Faculty and University Hospital, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | | | - Renaud Prudent
- Edelris, Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Christoph Peter
- Institute
of Molecular Medicine I, Medical Faculty and University Hospital, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Peter ‘t Hart
- Chemical
Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany,
| | - Herbert Waldmann
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany,Faculty
of Chemistry, Chemical Biology, Technical
University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany,
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20
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Feng D, Liu L, Shi Y, Du P, Xu S, Zhu Z, Xu J, Yao H. Current development of bicyclic peptides. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Luo J, Liu S, Lu H, Chen Q, Shi Y. A comprehensive review of microorganism-derived cyclic peptides: Bioactive functions and food safety applications. Compr Rev Food Sci Food Saf 2022; 21:5272-5290. [PMID: 36161470 DOI: 10.1111/1541-4337.13038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 01/28/2023]
Abstract
Cyclic peptides possess advanced structural characteristics of stability and play a vital role in medical treatment and agriculture. However, the biological functions of microorganism-derived cyclic peptides (MDCPs) and their applications in food industry were relatively absent. MDCPs are derived from extensive fermented food or soil. In this review, the synthesis approaches and structural characteristics are overviewed, while the interrelationship between bioactivities and functions is emphasized. This review summarizes the bioactivities of MDCPs from in vitro to in vivo, including antimicrobial activities, immune regulation, and antiviral cell activation. Their multiple functions as well as applications during food product processing, packaging, and storage are also comprehensively reviewed. Remarkably, some potential risks and cytotoxicity of MDCPs are also critically discussed. Moreover, future applications of MDCPs in the development of novel food additives and bioengineering materials are organized. Based on this review of native MDCPs, it is noteworthy that expected improvements of synthetic cyclic peptides in bioactive properties present potential valuable applications in future food, including artificial meat.
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Affiliation(s)
- Jiaqi Luo
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Siyu Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Hongyun Lu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Ying Shi
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
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22
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Ma B, Fan Y, Zhang D, Wei Y, Jian Y, Liu D, Wang Z, Gao Y, Ma J, Chen Y, Xu S, Li L. De Novo Design of an Androgen Receptor DNA Binding Domain-Targeted peptide PROTAC for Prostate Cancer Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201859. [PMID: 35971165 PMCID: PMC9534960 DOI: 10.1002/advs.202201859] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/10/2022] [Indexed: 05/27/2023]
Abstract
Androgen receptor splice variant-7 (AR-V7), one of the major driving factors, is the most attractive drug target in castration-resistant prostate cancer (CRPC). Currently, no available drugs efficiently target AR-V7 in clinical practice. The DNA binding domain (DBD) is indispensable for the transcriptional activity of AR full length and AR splice variants, including AR-V7. Based on the homodimerization structure of the AR DBD, a novel peptide-based proteolysis-targeting chimera (PROTAC) drug is designed to induce AR and AR-V7 degradation in a DBD and MDM2-dependent manner, without showing any activity on other hormone receptors. To overcome the short half-life and poor cell penetrability of peptide PROTAC drugs, an ultrasmall gold (Au)-peptide complex platform to deliver the AR DBD PROTAC in vivo is developed. The obtained Au-AR pep-PROTAC effectively degrades AR and AR-V7 in prostate cancer cell lines, particularly in CWR22Rv1 cells with DC50 values 48.8 and 79.2 nM, respectively. Au-AR pep-PROTAC results in suppression of AR levels and induces tumor regression in both enzalutamide sensitive and resistant prostate cancer animal models. Further optimization of the Au-AR pep-PROTAC can ultimately lead to a new therapy for AR-V7-positive CRPC.
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Affiliation(s)
- Bohan Ma
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Yizeng Fan
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Dize Zhang
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Yi Wei
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Yanlin Jian
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Donghua Liu
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Zixi Wang
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Yang Gao
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Jian Ma
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Yule Chen
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Shan Xu
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
| | - Lei Li
- Department of UrologyThe First Affiliated HospitalXi'an Jiaotong University#277 Yanta West RoadXi'anChina
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23
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Jacob B, Vogelaar A, Cadenas E, Camarero JA. Using the Cyclotide Scaffold for Targeting Biomolecular Interactions in Drug Development. Molecules 2022; 27:molecules27196430. [PMID: 36234971 PMCID: PMC9570680 DOI: 10.3390/molecules27196430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/28/2022] Open
Abstract
This review provides an overview of the properties of cyclotides and their potential for developing novel peptide-based therapeutics. The selective disruption of protein–protein interactions remains challenging, as the interacting surfaces are relatively large and flat. However, highly constrained polypeptide-based molecular frameworks with cell-permeability properties, such as the cyclotide scaffold, have shown great promise for targeting those biomolecular interactions. The use of molecular techniques, such as epitope grafting and molecular evolution employing the cyclotide scaffold, has shown to be highly effective for selecting bioactive cyclotides.
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Affiliation(s)
- Binu Jacob
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Alicia Vogelaar
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Enrique Cadenas
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 9033, USA
- Correspondence:
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24
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Pallara C, Cabot D, Rivas J, Brun S, Seco J, Abuasaker B, Tarragó T, Jaumot M, Prades R, Agell N. Peptidomimetics designed to bind to RAS effector domain are promising cancer therapeutic compounds. Sci Rep 2022; 12:15810. [PMID: 36138080 PMCID: PMC9499927 DOI: 10.1038/s41598-022-19703-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Oncogenic RAS proteins are important for driving tumour formation, and for maintenance of the transformed phenotype, and thus their relevance as a cancer therapeutic target is undeniable. We focused here on obtaining peptidomimetics, which have good pharmacological properties, to block Ras–effector interaction. Computational analysis was used to identify hot spots of RAS relevant for these interactions and to screen a library of peptidomimetics. Nine compounds were synthesized and assayed for their activity as RAS inhibitors in cultured cells. Most of them induced a reduction in ERK and AKT activation by EGF, a marker of RAS activity. The most potent inhibitor disrupted Raf and PI3K interaction with oncogenic KRAS, corroborating its mechanism of action as an inhibitor of protein–protein interactions, and thus validating our computational methodology. Most interestingly, improvement of one of the compounds allowed us to obtain a peptidomimetic that decreased the survival of pancreatic cancer cell lines harbouring oncogenic KRAS.
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Affiliation(s)
- Chiara Pallara
- Iproteos S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Debora Cabot
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, C/Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Josep Rivas
- Iproteos S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sonia Brun
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, C/Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jesús Seco
- Iproteos S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Baraa Abuasaker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, C/Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Teresa Tarragó
- Iproteos S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Montserrat Jaumot
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, C/Casanova 143, 08036, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Roger Prades
- Iproteos S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain.
| | - Neus Agell
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, C/Casanova 143, 08036, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
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25
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Nomura K, Hashimoto S, Takeyama R, Tamiya M, Kato T, Muraoka T, Kage M, Nii K, Kotake K, Iida S, Emura T, Tanada M, Iikura H. Broadly Applicable and Comprehensive Synthetic Method for N-Alkyl-Rich Drug-like Cyclic Peptides. J Med Chem 2022; 65:13401-13412. [DOI: 10.1021/acs.jmedchem.2c01296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Tatsuya Kato
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Terushige Muraoka
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kenichiro Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Satomi Iida
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Takashi Emura
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
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26
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Pei D. Designing Cell-Permeable Peptide Therapeutics That Enter the Cell by Endocytosis. ACS SYMPOSIUM SERIES. AMERICAN CHEMICAL SOCIETY 2022; 1417:179-197. [PMID: 37621949 PMCID: PMC10448808 DOI: 10.1021/bk-2022-1417.ch007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Intracellular protein-protein interactions (PPIs) represent a large class of exciting as well as challenging drug targets for traditional drug modalities (i.e., small molecules and biologics). Peptides (especially cyclic peptides) have proven highly effective as PPI inhibitors in vitro but are generally impermeable to the cell membrane. The recent discovery of a family of highly active cyclic cell-penetrating peptides (CPPs) has enabled the delivery of peptides into the cytosol of mammalian cells at therapeutically relevant levels. This chapter describes the various strategies that have been developed to conjugate or integrate different types of peptidyl cargoes (e.g., linear, cyclic, and stapled peptides) with cyclic CPPs to generate cell-permeable, metabolically stable, and biologically active macrocyclic peptides against intracellular targets including PPIs.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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27
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Mayer G, Shpilt Z, Kowalski H, Tshuva EY, Friedler A. Targeting Protein Interaction Hotspots Using Structured and Disordered Chimeric Peptide Inhibitors. ACS Chem Biol 2022; 17:1811-1823. [PMID: 35758642 DOI: 10.1021/acschembio.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The main challenge in inhibiting protein-protein interactions (PPI) for therapeutic purposes is designing molecules that bind specifically to the interaction hotspots. Adding to the complexity, such hotspots can be within both structured and disordered interaction interfaces. To address this, we present a strategy for inhibiting the structured and disordered hotspots of interactions using chimeric peptides that contain both structured and disordered parts. The chimeric peptides we developed are comprised of a cyclic structured part and a disordered part, which target both disordered and structured hotspots. We demonstrate our approach by developing peptide inhibitors for the interactions of the antiapoptotic iASPP protein. First, we developed a structured, α-helical stapled peptide inhibitor, derived from the N-terminal domain of MDM2. The peptide bound two hotspots on iASPP at the low micromolar range and had a cytotoxic effect on A2780 cancer cells with a half-maximal inhibitory concentration (IC50) value of 10 ± 1 μM. We then developed chimeric peptides comprising the structured stapled helical peptide and the disordered p53-derived LinkTer peptide that we previously showed to inhibit iASPP by targeting its disordered RT loop. The chimeric peptide targeted both structured and disordered domains in iASPP with higher affinity compared to the individual structured and disordered peptides and caused cancer cell death. Our strategy overcomes the inherent difficulty in inhibiting the interactions of proteins that possess structured and disordered regions. It does so by using chimeric peptides derived from different interaction partners that together target a much wider interface covering both the structured and disordered domains. This paves the way for developing such inhibitors for therapeutic purposes.
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Affiliation(s)
- Guy Mayer
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zohar Shpilt
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hadar Kowalski
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Edit Y Tshuva
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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28
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Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
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Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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29
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Buyanova M, Pei D. Targeting intracellular protein-protein interactions with macrocyclic peptides. Trends Pharmacol Sci 2022; 43:234-248. [PMID: 34911657 PMCID: PMC8840965 DOI: 10.1016/j.tips.2021.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for traditional drug modalities. Macrocyclic peptides (MPs) prove highly effective PPI inhibitors in vitro and can be rapidly discovered against PPI targets by rational design or screening combinatorial libraries but are generally impermeable to the cell membrane. Recent advances in MP science and technology are allowing for the development of 'drug-like' MPs that potently and specifically modulate intracellular PPI targets in cell culture and animal models. In this review, we highlight recent progress in generating cell-permeable MPs that enter the mammalian cell by passive diffusion, endocytosis followed by endosomal escape, or as-yet unknown mechanisms.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
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30
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Chen T, Sun T, Bian Y, Pei Y, Feng F, Chi H, Li Y, Tang X, Sang S, Du C, Chen Y, Chen Y, Sun H. The Design and Optimization of Monomeric Multitarget Peptides for the Treatment of Multifactorial Diseases. J Med Chem 2022; 65:3685-3705. [DOI: 10.1021/acs.jmedchem.1c01456] [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]
Affiliation(s)
- Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Tianyu Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yaoyao Bian
- College of Acupuncture and Massage, College of Regimen and Rehabilitation, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Yuqiong Pei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Feng Feng
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Heng Chi
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Yuan Li
- Department of Pharmaceutical Engineering, Jiangsu Food and Pharmaceuticals Science College, Huaian 223005, People’s Republic of China
| | - Xu Tang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Shenghu Sang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Chenxi Du
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Ying Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
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31
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Screening of diverse marine invertebrate extracts identified Lissoclinotoxin F, Discodermin B, and other anti-Mycobacterium tuberculosis active compounds. J Antibiot (Tokyo) 2022; 75:213-225. [DOI: 10.1038/s41429-022-00507-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/10/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
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32
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Bacon K, Menegatti S, Rao BM. Discovery of Cyclic Peptide Binders from Chemically Constrained Yeast Display Libraries. Methods Mol Biol 2022; 2491:387-415. [PMID: 35482201 DOI: 10.1007/978-1-0716-2285-8_20] [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: 06/14/2023]
Abstract
Cyclic peptides with engineered protein-binding activity have great potential as therapeutic and diagnostic reagents owing to their favorable properties, including high affinity and selectivity. Cyclic peptide binders have generally been isolated from phage display combinatorial libraries utilizing panning based selections. As an alternative, we have developed a yeast surface display platform to identify and characterize cyclic peptide binders from genetically encoded combinatorial libraries. Through a combination of magnetic selection and fluorescence-activated cell sorting (FACS), high-affinity cyclic peptide binders can be efficiently isolated from yeast display libraries. In this platform, linear peptide precursors are expressed as yeast surface fusions. To achieve cyclization of the linear precursors, the cells are incubated with disuccinimidyl glutarate, which crosslinks amine groups within the displayed linear peptide sequence. Here, we detail protocols for cyclizing linear peptides expressed as yeast surface fusions. We also discuss how to synthesize a yeast display library of linear peptide precursors. Subsequently, we provide suggestions on how to utilize magnetic selections and FACS to isolate cyclic peptide binders for target proteins of interest from a peptide combinatorial library. Lastly, we detail how yeast surface displayed cyclic peptides can be used to obtain efficient estimates of binding affinity, eliminating the need for chemically synthesized peptides when performing mutant characterization.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA.
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33
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Wu C, Hoang HN, Hill TA, Lim J, Kok WM, Akondi K, Liu L, Fairlie DP. Helical structure in cyclic peptides: effect of N-methyl amides versus esters. Chem Commun (Camb) 2022; 58:12475-12478. [DOI: 10.1039/d2cc05092g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic peptides with esters but not N-methyl amides are the smallest known alpha helices in water and can enter cells.
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Affiliation(s)
- Chongyang Wu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Huy N. Hoang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Timothy A. Hill
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Junxian Lim
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - W. Mei Kok
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Kalyani Akondi
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Ligong Liu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - David P. Fairlie
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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34
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Chen KE, Guo Q, Hill TA, Cui Y, Kendall AK, Yang Z, Hall RJ, Healy MD, Sacharz J, Norwood SJ, Fonseka S, Xie B, Reid RC, Leneva N, Parton RG, Ghai R, Stroud DA, Fairlie DP, Suga H, Jackson LP, Teasdale RD, Passioura T, Collins BM. De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. SCIENCE ADVANCES 2021; 7:eabg4007. [PMID: 34851660 PMCID: PMC8635440 DOI: 10.1126/sciadv.abg4007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/14/2021] [Indexed: 05/27/2023]
Abstract
The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function.
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Affiliation(s)
- Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Timothy A. Hill
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yi Cui
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Zhe Yang
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ryan J. Hall
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael D. Healy
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Joanna Sacharz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Suzanne J. Norwood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sachini Fonseka
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert C. Reid
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Queensland, Australia
| | - Rajesh Ghai
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - David A. Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Rohan D. Teasdale
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- Sydney Analytical, School of Life and Environmental Sciences and School of Chemistry, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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35
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Hostetler MA, Smith C, Nelson S, Budimir Z, Modi R, Woolsey I, Frerk A, Baker B, Gantt J, Parkinson EI. Synthetic Natural Product Inspired Cyclic Peptides. ACS Chem Biol 2021; 16:2604-2611. [PMID: 34699170 PMCID: PMC8610019 DOI: 10.1021/acschembio.1c00641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Natural products
are a bountiful source of bioactive molecules.
Unfortunately, discovery of novel bioactive natural products is challenging
due to cryptic biosynthetic gene clusters, low titers, and arduous
purifications. Herein, we describe SNaPP (Synthetic Natural Product
Inspired Cyclic Peptides), a method for identifying
NP-inspired bioactive peptides. SNaPP expedites bioactive molecule
discovery by combining bioinformatics predictions of nonribosomal
peptide synthetases with chemical synthesis of the predicted natural
products (pNPs). SNaPP utilizes a recently discovered cyclase, the
penicillin binding protein-like cyclase, as the lynchpin for the development
of a library of head-to-tail cyclic peptide pNPs. Analysis of 500
biosynthetic gene clusters allowed for identification of 131 novel
pNPs. Fifty-one diverse pNPs were synthesized using solid phase peptide
synthesis and solution-phase cyclization. Antibacterial testing revealed
14 pNPs with antibiotic activity, including activity against multidrug-resistant
Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining
bioinformatics predictions with chemical synthesis to accelerate the
discovery of bioactive molecules.
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Affiliation(s)
- Matthew A. Hostetler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chloe Smith
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zachary Budimir
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ian Woolsey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Autumn Frerk
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Braden Baker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jessica Gantt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth I. Parkinson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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36
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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37
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Sanner MF, Dieguez L, Forli S, Lis E. Improving Docking Power for Short Peptides Using Random Forest. J Chem Inf Model 2021; 61:3074-3090. [PMID: 34124893 PMCID: PMC8543977 DOI: 10.1021/acs.jcim.1c00573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In recent years, therapeutic peptides have gained a lot interest as demonstrated by the 60 peptides approved as drugs in major markets and 150+ peptides currently in clinical trials. However, while small molecule docking is routinely used in rational drug design efforts, docking peptides has proven challenging partly because docking scoring functions, developed and calibrated for small molecules, perform poorly for these molecules. Here, we present random forest classifiers trained to discriminate correctly docked peptides. We show that, for a testing set of 47 protein-peptide complexes, structurally dissimilar from the training set and previously used to benchmark AutoDock Vina's ability to dock short peptides, these random forest classifiers improve docking power from ∼25% for AutoDock scoring functions to an average of ∼70%. These results pave the way for peptide-docking success rates comparable to those of small molecule docking. To develop these classifiers, we compiled the ProptPep37_2021 data set, a curated, high-quality set of 322 crystallographic protein-peptides complexes annotated with structural similarity information. The data set also provides a collection of high-quality putative poses with a range of deviations from the crystallographic pose, providing correct and incorrect poses (i.e., decoys) of the peptide for each entry. The ProptPep37_2021 data set as well as the classifiers presented here are freely available.
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Affiliation(s)
- Michel F. Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 93037, USA
| | - Leonard Dieguez
- Koliber Biosciences Inc., 12265 World Trade Drive, Suite G, San Diego, CA 92128, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 93037, USA
| | - Ewa Lis
- Koliber Biosciences Inc., 12265 World Trade Drive, Suite G, San Diego, CA 92128, USA
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38
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Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
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Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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39
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Norman A, Franck C, Christie M, Hawkins PME, Patel K, Ashhurst AS, Aggarwal A, Low JKK, Siddiquee R, Ashley CL, Steain M, Triccas JA, Turville S, Mackay JP, Passioura T, Payne RJ. Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display. ACS CENTRAL SCIENCE 2021; 7:1001-1008. [PMID: 34230894 PMCID: PMC8189037 DOI: 10.1021/acscentsci.0c01708] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 05/03/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality, and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein, and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (K D) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect the spike protein in solution by ELISA, and the cocrystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a β-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD, and the ligands discovered in this work may find future use as reagents for diagnostic applications.
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Affiliation(s)
- Alexander Norman
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Charlotte Franck
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary Christie
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paige M. E. Hawkins
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Karishma Patel
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anneliese S. Ashhurst
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Jason K. K. Low
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rezwan Siddiquee
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Caroline L. Ashley
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Megan Steain
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James A. Triccas
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joel P. Mackay
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
| | - Toby Passioura
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Analytical, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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40
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Nubbemeyer B, Pepanian A, Paul George AA, Imhof D. Strategies towards Targeting Gαi/s Proteins: Scanning of Protein-Protein Interaction Sites To Overcome Inaccessibility. ChemMedChem 2021; 16:1696-1715. [PMID: 33615736 PMCID: PMC8252600 DOI: 10.1002/cmdc.202100039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 12/16/2022]
Abstract
Heterotrimeric G proteins are classified into four subfamilies and play a key role in signal transduction. They transmit extracellular signals to intracellular effectors subsequent to the activation of G protein-coupled receptors (GPCRs), which are targeted by over 30 % of FDA-approved drugs. However, addressing G proteins as drug targets represents a compelling alternative, for example, when G proteins act independently of the corresponding GPCRs, or in cases of complex multifunctional diseases, when a large number of different GPCRs are involved. In contrast to Gαq, efforts to target Gαi/s by suitable chemical compounds has not been successful so far. Here, a comprehensive analysis was conducted examining the most important interface regions of Gαi/s with its upstream and downstream interaction partners. By assigning the existing compounds and the performed approaches to the respective interfaces, the druggability of the individual interfaces was ranked to provide perspectives for selective targeting of Gαi/s in the future.
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Affiliation(s)
- Britta Nubbemeyer
- Pharmaceutical Biochemistry and BioanalyticsPharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Anna Pepanian
- Pharmaceutical Biochemistry and BioanalyticsPharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
| | | | - Diana Imhof
- Pharmaceutical Biochemistry and BioanalyticsPharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
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41
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Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool. Mar Drugs 2021; 19:md19060311. [PMID: 34072121 PMCID: PMC8229464 DOI: 10.3390/md19060311] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.
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42
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Ge Y, Zhang S, Erdelyi M, Voelz VA. Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2. J Chem Inf Model 2021; 61:2353-2367. [PMID: 33905247 PMCID: PMC9960209 DOI: 10.1021/acs.jcim.1c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding mechanisms of protein folding and binding is crucial to designing their molecular function. Molecular dynamics (MD) simulations and Markov state model (MSM) approaches provide a powerful way to understand complex conformational change that occurs over long time scales. Such dynamics are important for the design of therapeutic peptidomimetic ligands, whose affinity and binding mechanism are dictated by a combination of folding and binding. To examine the role of preorganization in peptide binding to protein targets, we performed massively parallel explicit-solvent MD simulations of cyclic β-hairpin ligands designed to mimic the p53 transactivation domain and competitively bind mouse double minute 2 homologue (MDM2). Disrupting the MDM2-p53 interaction is a therapeutic strategy to prevent degradation of the p53 tumor suppressor in cancer cells. MSM analysis of over 3 ms of aggregate trajectory data enabled us to build a detailed mechanistic model of coupled folding and binding of four cyclic peptides which we compare to experimental binding affinities and rates. The results show a striking relationship between the relative preorganization of each ligand in solution and its affinity for MDM2. Specifically, changes in peptide conformational populations predicted by the MSMs suggest that entropy loss upon binding is the main factor influencing affinity. The MSMs also enable detailed examination of non-native interactions which lead to misfolded states and comparison of structural ensembles with experimental NMR measurements. In contrast to an MSM study of p53 transactivation domain (TAD) binding to MDM2, MSMs of cyclic β-hairpin binding show a conformational selection mechanism. Finally, we make progress toward predicting accurate off rates of cyclic peptides using multiensemble Markov models (MEMMs) constructed from unbiased and biased simulated trajectories.
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Affiliation(s)
- Yunui Ge
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
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43
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Moritsugu K, Takeuchi K, Kamiya N, Higo J, Yasumatsu I, Fukunishi Y, Fukuda I. Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. J Chem Inf Model 2021; 61:1921-1930. [PMID: 33835817 DOI: 10.1021/acs.jcim.0c01427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantifying the cell permeability of cyclic peptides is crucial for their rational drug design. However, the reasons remain unclear why a minor chemical modification, such as the difference between Ras inhibitors cyclorasin 9A5 and 9A54, can substantially change a peptide's permeability. To address this question, we performed enhanced sampling simulations of these two 11-mer peptides using the coupled Nosé-Hoover equation (cNH) we recently developed. The present cNH simulations realized temperature fluctuations over a wide range (240-600 K) in a dynamic manner, allowing structural samplings that were well validated by nuclear Overhauser effect measurements. The derived structural ensembles were comprehensively analyzed by all-atom structural clustering, mapping the derived clusters onto principal components (PCs) that characterize the cyclic structure, and calculating cluster-dependent geometric and chemical properties. The planar-open conformation was dominant in aqueous solvent, owing to inclusion of the Trp side chain in the main-chain ring, while the compact-closed conformation, which favors cell permeation due to its compactness and high polarity, was also accessible. Conformation-dependent cell permeability was observed in one of the derived PCs, demonstrating that decreased cell permeability in 9A54 is due to the high free energy barrier separating the two conformations. The origin of the change in free energy surface was determined to be loss of flexibility in the modified residues 2-3, resulting from the increased bulkiness of their side chains. The derived molecular mechanism of cell permeability highlights the significance of complete structural dynamics surveys for accelerating drug development with cyclic peptides.
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Affiliation(s)
- Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Isao Yasumatsu
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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44
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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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45
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Huang H, Damjanovic J, Miao J, Lin YS. Cyclic peptides: backbone rigidification and capability of mimicking motifs at protein-protein interfaces. Phys Chem Chem Phys 2021; 23:607-616. [PMID: 33331371 DOI: 10.1039/d0cp04633g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cyclization is commonly employed in efforts to improve the target binding affinity of peptide-based probes and therapeutics. Many structural motifs have been identified at protein-protein interfaces and provide promising targets for inhibitor design using cyclic peptides. Cyclized peptides are generally assumed to be rigidified relative to their linear counterparts. This rigidification potentially pre-organizes the molecules to interact properly with their targets. However, the actual impact of cyclization on, for example, peptide configurational entropy, is currently poorly understood in terms of both its magnitude and molecular-level origins. Moreover, even with thousands of desired structural motifs at hand, it is currently not possible to a priori identify the ones that are most promising to mimic using cyclic peptides nor to select the ideal linker length. Instead, labor-intensive chemical synthesis and experimental characterization of various cyclic peptide designs are required, in hopes of finding one with improved target affinity. Herein, using molecular dynamics simulations of polyglycines, we elucidated how head-to-tail cyclization impacts peptide backbone dihedral entropy and developed a simple strategy to rapidly screen for structures that can be reliably mimicked by preorganized cyclic peptides. As expected, cyclization generally led to a reduction in backbone dihedral entropy; notably, however, this effect was minimal when the length of polyglycines was >9 residues. We also found that the reduction in backbone dihedral entropy upon cyclization of small polyglycine peptides does not result from more restricted distributions of the dihedrals; rather, it was the correlations between specific dihedrals that caused the decrease in configurational entropy in the cyclic peptides. Using our comprehensive cyclo-Gn structural ensembles, we obtained a holistic picture of what conformations are accessible to cyclic peptides. Using "hot loops" recently identified at protein-protein interfaces as an example, we provide clear guidelines for choosing the "easiest" hot loops for cyclic peptides to mimic and for identifying appropriate cyclic peptide lengths. In conclusion, our results provide an understanding of the thermodynamics and structures of this interesting class of molecules. This information should prove particularly useful for designing cyclic peptide inhibitors of protein-protein interactions.
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Affiliation(s)
- He Huang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
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46
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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47
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Zhang M, Xu B, Li N, Liu H, Shi X, Zhang Q, Shi Y, Xu K, Xiao J, Chen D, Zhu H, Sun Y, Zhang T, Zhang R, Fang Q. Synthesis and Biological Characterization of Cyclic Disulfide-Containing Peptide Analogs of the Multifunctional Opioid/Neuropeptide FF Receptor Agonists That Produce Long-Lasting and Nontolerant Antinociception. J Med Chem 2020; 63:15709-15725. [PMID: 33271020 DOI: 10.1021/acs.jmedchem.0c01367] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In a previously described chimeric peptide, we reported that the multifunctional opioid/neuropeptide FF (NPFF) receptor agonist 0 (BN-9) produced antinociception for 1.5 h after supraspinal administration. Herein, four cyclic disulfide analogs containing l- and/or d-type cysteine at positions 2 and 5 were synthesized. The cyclized analogs and their linear counterparts behaved as multifunctional agonists at both opioid and NPFF receptors in vitro and produced potent analgesia without tolerance development. In comparison to 0, cyclized peptide 6 exhibited sevenfold more potent μ-opioid receptor agonistic activity in vitro. Interestingly, the cyclized analog 6 possessed an improved stability in the brain and an increased blood-brain barrier permeability compared to the parent peptide 0 and produced more potent analgesia after supraspinal or subcutaneous administration with improved duration of action of 4 h. In addition, antinociceptive tolerance of analog 6 was greatly reduced after subcutaneous injection compared to fentanyl, as was the rewarding effect, withdrawal reaction, and gastrointestinal inhibition.
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Affiliation(s)
- Mengna Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Biao Xu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Ning Li
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Hui Liu
- School of Pharmacy, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Xuerui Shi
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Qinqin Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Yanbin Shi
- School of Pharmacy, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Kangtai Xu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Jian Xiao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Dan Chen
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Hanwen Zhu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Yulong Sun
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710000, PR China
| | - Ting Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Run Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
| | - Quan Fang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, and Institute of Physiology, School of Basic Medical Sciences, Lanzhou University, 199 Donggang West Road, Lanzhou 730000, PR China
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48
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew Chem Int Ed Engl 2020; 59:21571-21577. [PMID: 32789999 PMCID: PMC7719619 DOI: 10.1002/anie.202004550] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Large macrocyclic peptides can achieve surprisingly high membrane permeability, although the properties that govern permeability in this chemical space are only beginning to come into focus. We generated two libraries of cyclic decapeptides with stable cross-β conformations, and found that peptoid substitutions within the β-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing β-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water. Both rigid and chameleonic compounds showed high permeability over a wide lipophilicity range, with peak permeabilities differing significantly depending on scaffold rigidity. Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides, and that scaffold rigidity can be used to tune optimal lipophilicity.
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Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Joshua Schwochert
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alexandra C. Turmon
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Victoria G. Klein
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - Okimasa Okada
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
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49
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Dougherty PG, Karpurapu M, Koley A, Lukowski JK, Qian Z, Nirujogi TS, Rusu L, Chung S, Hummon AB, Li HW, Christman JW, Pei D. A Peptidyl Inhibitor that Blocks Calcineurin-NFAT Interaction and Prevents Acute Lung Injury. J Med Chem 2020; 63:12853-12872. [PMID: 33073986 PMCID: PMC8011862 DOI: 10.1021/acs.jmedchem.0c01236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is an inflammatory lung disease with a high morbidity and mortality rate, for which no pharmacologic treatment is currently available. Our previous studies discovered that a pivotal step in the disease process is the activation of the nuclear factor of activated T cells (NFAT) c3 in lung macrophages, suggesting that inhibitors against the upstream protein phosphatase calcineurin should be effective for prevention/treatment of ARDS. Herein, we report the development of a highly potent, cell-permeable, and metabolically stable peptidyl inhibitor, CNI103, which selectively blocks the interaction between calcineurin and NFATc3, through computational and medicinal chemistry. CNI103 specifically inhibited calcineurin signaling in vitro and in vivo and exhibited a favorable pharmacokinetic profile, broad tissue distribution following different routes of administration, and minimal toxicity. Our data indicate that CNI103 is a promising novel treatment for ARDS and other inflammatory diseases.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Manjula Karpurapu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
| | - Jessica K. Lukowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Teja Srinivas Nirujogi
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
- East Liverpool City Hospital, 425 W 5th Street, East Liverpool, Ohio 43920, United States
| | - Luiza Rusu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Sangwoon Chung
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus OH, 43210, United States
| | - Hao W. Li
- Columbia Center for Translational Immunology, Columbia University, 650 W. 168 Street, New York, New York 10032, United States
| | - John W. Christman
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
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50
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Simon‐Gracia L, Savier E, Parizot C, Brossas JY, Loisel S, Teesalu T, Conti F, Charlotte F, Scatton O, Aoudjehane L, Rebollo A. Bifunctional Therapeutic Peptides for Targeting Malignant B Cells and Hepatocytes: Proof of Concept in Chronic Lymphocytic Leukemia. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lorena Simon‐Gracia
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine University of Tartu Tartu 50411 Estonia
| | - Eric Savier
- Department of Hepatobiliary and Liver Transplantation Surgery, AP‐HP Pitié‐Salpêtrière Hospital Paris 75013 France
- Sorbonne Université INSERM, ICAN Paris 75006 France
| | - Christophe Parizot
- Department of Immunology, AP‐HP Pitié‐Salpêtrière Hospital Paris 75013 France
| | - Jean Yves Brossas
- Department of Parasitology, AP‐HP Pitié‐Salpêtrière Hospital Paris 75013 France
| | - Severine Loisel
- Service Général des plateformes, Animalerie Commune Université de Brest Brest 29238 France
| | - Tambet Teesalu
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine University of Tartu Tartu 50411 Estonia
- Cancer Research Center Sanford Burnham Prebys Medical Discovery Institute La Jolla CA 92037 USA
- Center for Nanomedicine University of California Santa Barbara CA 93106 USA
| | - Filomena Conti
- Sorbonne Université INSERM, ICAN Paris 75006 France
- Department of Medical Liver Transplantation AP‐HP Pitié‐Salpêtrière Paris 75013 France
| | - Frederic Charlotte
- Department of Anatomophatoloty, AP‐HP Pitié‐Salpêtrière Hospital Paris 75013 France
| | - Olivier Scatton
- Department of Hepatobiliary and Liver Transplantation Surgery, AP‐HP Pitié‐Salpêtrière Hospital Paris 75013 France
| | | | - Angelita Rebollo
- Inserm U1267, CNRS‐UMR 8258, Faculté de Pharmacie Paris 75006 France
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