1
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Wu J, Wang Y, Cai W, Chen D, Peng X, Dong H, Li J, Liu H, Shi S, Tang S, Li Z, Sui H, Wang Y, Wu C, Zhang Y, Fu X, Yin Y. Ribosomal translation of fluorinated non-canonical amino acids for de novo biologically active fluorinated macrocyclic peptides. Chem Sci 2024:d4sc04061a. [PMID: 39129776 PMCID: PMC11310889 DOI: 10.1039/d4sc04061a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024] Open
Abstract
Fluorination has emerged as a promising strategy in medicinal chemistry to improve the pharmacological profiles of drug candidates. Similarly, incorporating fluorinated non-canonical amino acids into macrocyclic peptides expands chemical diversity and enhances their pharmacological properties, from improved metabolic stability to enhanced cell permeability and target interactions. However, only a limited number of fluorinated non-canonical amino acids, which are canonical amino acid analogs, have been incorporated into macrocyclic peptides by ribosomes for de novo construction and target-based screening of fluorinated macrocyclic peptides. In this study, we report the ribosomal translation of a series of distinct fluorinated non-canonical amino acids, including mono-to tri-fluorinated variants, as well as fluorinated l-amino acids, d-amino acids, β-amino acids, etc. This enabled the de novo discovery of fluorinated macrocyclic peptides with high affinity for EphA2, and particularly the identification of those exhibiting broad-spectrum activity against Gram-negative bacteria by targeting the BAM complex. This study not only expands the scope of ribosomally translatable fluorinated amino acids but also underscores the versatility of fluorinated macrocyclic peptides as potent therapeutic agents.
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Affiliation(s)
- Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Yuchan Wang
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Wenfeng Cai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Danyan Chen
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Xiangda Peng
- Shanghai Zelixir Biotech Company Ltd Shanghai 200030 China
| | - Huilei Dong
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Jinjing Li
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Hongtan Liu
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Shuting Shi
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Sen Tang
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Zhifeng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Haiyan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Yan Wang
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Chuanliu Wu
- College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
| | - Xinmiao Fu
- College of Life Sciences, Fujian Normal University Fuzhou 350117 China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University Qingdao 266237 China
- Shandong Research Institute of Industrial Technology Jinan 250101 China
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2
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Pierzynowska K, Morcinek-Orłowska J, Gaffke L, Jaroszewicz W, Skowron PM, Węgrzyn G. Applications of the phage display technology in molecular biology, biotechnology and medicine. Crit Rev Microbiol 2024; 50:450-490. [PMID: 37270791 DOI: 10.1080/1040841x.2023.2219741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 10/17/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The phage display technology is based on the presentation of peptide sequences on the surface of virions of bacteriophages. Its development led to creation of sophisticated systems based on the possibility of the presentation of a huge variability of peptides, attached to one of proteins of bacteriophage capsids. The use of such systems allowed for achieving enormous advantages in the processes of selection of bioactive molecules. In fact, the phage display technology has been employed in numerous fields of biotechnology, as diverse as immunological and biomedical applications (in both diagnostics and therapy), the formation of novel materials, and many others. In this paper, contrary to many other review articles which were focussed on either specific display systems or the use of phage display in selected fields, we present a comprehensive overview of various possibilities of applications of this technology. We discuss an usefulness of the phage display technology in various fields of science, medicine and the broad sense of biotechnology. This overview indicates the spread and importance of applications of microbial systems (exemplified by the phage display technology), pointing to the possibility of developing such sophisticated tools when advanced molecular methods are used in microbiological studies, accompanied with understanding of details of structures and functions of microbial entities (bacteriophages in this case).
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Weronika Jaroszewicz
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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3
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Witzdam L, White T, Rodriguez-Emmenegger C. Steps Toward Recapitulating Endothelium: A Perspective on the Next Generation of Hemocompatible Coatings. Macromol Biosci 2024:e2400152. [PMID: 39072925 DOI: 10.1002/mabi.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/26/2024] [Indexed: 07/30/2024]
Abstract
Endothelium, the lining in this blood vessel, orchestrates three main critical functions such as protecting blood components, modulating of hemostasis by secreting various inhibitors, and directing clot digestion (fibrinolysis) by activating tissue plasminogen activator. No other surface can perform these tasks; thus, the contact of blood and blood-contacting medical devices inevitably leads to the activation of coagulation, often causing device failure, and thromboembolic complications. This perspective, first, discusses the biological mechanisms of activation of coagulation and highlights the efforts of advanced coatings to recapitulate one characteristic of endothelium, hereafter single functions of endothelium and noting necessity of the synergistic integration of its three main functions. Subsequently, it is emphasized that to overcome the challenges of blood compatibility an endothelium-mimicking system is needed, proposing a synergy of bottom-up synthetic biology, particularly synthetic cells, with passive- and bioactive surface coatings. Such integration holds promise for developing advanced biomaterials capable of recapitulating endothelial functions, thereby enhancing the hemocompatibility and performance of blood-contacting medical devices.
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Affiliation(s)
- Lena Witzdam
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac, 10, 12, Barcelona, 08028, Spain
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Tom White
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac, 10, 12, Barcelona, 08028, Spain
| | - Cesar Rodriguez-Emmenegger
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac, 10, 12, Barcelona, 08028, Spain
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
- Biomedical Research Networking, Center in Bioengineering, Biomaterials and Nanomedicine, The Institute of Health Carlos III, Madrid, 28029, Spain
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4
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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5
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Ito K, Matsuda Y, Mine A, Miyairi K, Kikuchi Y, Konishi A. Bacterially Secretable Single-Chain Tandem Macrocyclic Peptides for High Affinity and Inhibitory Activity. Chembiochem 2023; 24:e202200599. [PMID: 36409290 DOI: 10.1002/cbic.202200599] [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: 10/19/2022] [Revised: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The inhibition of protein-protein interactions (PPIs) is an effective approach for therapy. Owing to their large binding surface areas to target proteins, macrocyclic peptides are suitable molecules for PPI inhibition. In this study, we developed single-chain tandem macrocyclic peptides (STaMPtides) that inhibits the vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2). They were artificially designed to comprise two different VEGFR2-binding macrocyclic peptides linked in tandem by peptide linkers and secreted by Corynebacterium glutamicum. Most potent VEGFR2-inhibitory STaMPtides with length-optimized linkers exhibited >1000 times stronger inhibitory activity than their parental monomeric peptides, possibly due to the avidity effect of heterodimerization. Our approach of using STaMPtides for PPI inhibition may be used to inhibit other extracellular factors, such as growth factors and cytokines.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
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6
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Frolov AI, Chankeshwara SV, Abdulkarim Z, Ghiandoni GM. pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides. J Chem Inf Model 2023; 63:187-196. [PMID: 36573842 PMCID: PMC9832473 DOI: 10.1021/acs.jcim.2c01261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The isoelectric point (pI) is a fundamental physicochemical property of peptides and proteins. It is widely used to steer design away from low solubility and aggregation and guide peptide separation and purification. Experimental measurements of pI can be replaced by calculations knowing the ionizable groups of peptides and their corresponding pKa values. Different pKa sets are published in the literature for natural amino acids, however, they are insufficient to describe synthetically modified peptides, complex peptides of natural origin, and peptides conjugated with structures of other modalities. Noncanonical modifications (nCAAs) are ignored in the conventional sequence-based pI calculations, therefore producing large errors in their pI predictions. In this work, we describe a pI calculation method that uses the chemical structure as an input, automatically identifies ionizable groups of nCAAs and other fragments, and performs pKa predictions for them. The method is validated on a curated set of experimental measures on 29 modified and 119093 natural peptides, providing an improvement of R2 from 0.74 to 0.95 and 0.96 against the conventional sequence-based approach for modified peptides for the two studied pKa prediction tools, ACDlabs and pKaMatcher, correspondingly. The method is available in the form of an open source Python library at https://github.com/AstraZeneca/peptide-tools, which can be integrated into other proprietary and free software packages. We anticipate that the pI calculation tool may facilitate optimization and purification activities across various application domains of peptides, including the development of biopharmaceuticals.
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Affiliation(s)
- Andrey I. Frolov
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D,
AstraZeneca, Gothenburg, Sweden,
| | - Sunay V. Chankeshwara
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D,
AstraZeneca, Gothenburg, Sweden
| | - Zeyed Abdulkarim
- Early
Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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7
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Tian S, Durek T, Wang CK, Zdenek CN, Fry BG, Craik DJ, de Veer SJ. Engineering the Cyclization Loop of MCoTI-II Generates Targeted Cyclotides that Potently Inhibit Factor XIIa. J Med Chem 2022; 65:15698-15709. [PMID: 36383928 DOI: 10.1021/acs.jmedchem.2c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Factor XIIa (FXIIa) is a promising target for developing new drugs that prevent thrombosis without causing bleeding complications. A native cyclotide (MCoTI-II) is gaining interest for engineering FXIIa-targeted anticoagulants as this peptide inhibits FXIIa but not other coagulation proteases. Here, we engineered the native biosynthetic cyclization loop of MCoTI-II (loop 6) to generate improved FXIIa inhibitors. Decreasing the loop length led to gains in potency up to 7.7-fold, with the most potent variant having five residues in loop 6 (Ki = 25 nM). We subsequently examined sequence changes within loop 6 and an adjacent loop, with substitutions at P4 and P2' producing a potent FXIIa inhibitor (Ki = 2 nM) that displayed more than 700-fold selectivity, was stable in human serum, and blocked the intrinsic coagulation pathway in human plasma. These findings demonstrate that engineering the biosynthetic cyclization loop can generate improved cyclotide variants, expanding their potential for drug discovery.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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8
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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9
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Liu W, de Veer SJ, Huang YH, Sengoku T, Okada C, Ogata K, Zdenek CN, Fry BG, Swedberg JE, Passioura T, Craik DJ, Suga H. An Ultrapotent and Selective Cyclic Peptide Inhibitor of Human β-Factor XIIa in a Cyclotide Scaffold. J Am Chem Soc 2021; 143:18481-18489. [PMID: 34723512 DOI: 10.1021/jacs.1c07574] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclotides are plant-derived peptides with complex structures shaped by their head-to-tail cyclic backbone and cystine knot core. These structural features underpin the native bioactivities of cyclotides, as well as their beneficial properties as pharmaceutical leads, including high proteolytic stability and cell permeability. However, their inherent structural complexity presents a challenge for cyclotide engineering, particularly for accessing libraries of sufficient chemical diversity to design potent and selective cyclotide variants. Here, we report a strategy using mRNA display enabling us to select potent cyclotide-based FXIIa inhibitors from a library comprising more than 1012 members based on the cyclotide scaffold of Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II). The most potent and selective inhibitor, cMCoFx1, has a pM inhibitory constant toward FXIIa with greater than three orders of magnitude selectivity over related serine proteases, realizing specific inhibition of the intrinsic coagulation pathway. The cocrystal structure of cMCoFx1 and FXIIa revealed interactions at several positions across the contact interface that conveyed high affinity binding, highlighting that such cyclotides are attractive cystine knot scaffolds for therapeutic development.
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Affiliation(s)
- Wenyu Liu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Simon J de Veer
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yen-Hua Huang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,School of Life and Environmental Sciences, School of Chemistry and Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Craik
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia
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10
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Abstract
Introduction: Blood coagulation factor XII (FXII) is an emerging and potentially safe drug target, which dysregulation is associated with thrombosis, hereditary angioedema, and (neuro)inflammation. At the same time, FXII-deficiency is practically asymptomatic. Industrial and academic institutions have developed a number of potential therapeutic agents targeting either FXII zymogen or its active form FXIIa for the treatment of thrombotic and inflammatory conditions associated with the activity of this enzyme.Areas covered: A short overview of the FXII(a) structure and function, underlining its suitability as a drug target, is given. The article reviews patents reported over the last three decades on FXII(a)-targeting therapeutic agents. These agents include small molecules, proteins, peptides, oligonucleotides, siRNAs, and monoclonal antibodies.Expert opinion: The performed analysis of patents revealed that many FXII(a) inhibitors are in the early preclinical stage, while several already showed efficacy in vivo animal models of thrombosis, sepsis, hereditary angioedema, and multiple sclerosis. Two anti-FXIIa agents namely tick protein Ir-CPI and monoclonal antibody CSL312 are currently in human clinical trials. The results of these trials and further studies of FXII(a) pathophysiological functions will encourage the development of new FXII(a) inhibitors.
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Affiliation(s)
- Dmitrii V Kalinin
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
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11
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Ford DJ, Duggan NM, Fry SE, Ripoll-Rozada J, Agten SM, Liu W, Corcilius L, Hackeng TM, van Oerle R, Spronk HMH, Ashhurst AS, Mini Sasi V, Kaczmarski JA, Jackson CJ, Pereira PJB, Passioura T, Suga H, Payne RJ. Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming. J Med Chem 2021; 64:7853-7876. [PMID: 34044534 DOI: 10.1021/acs.jmedchem.1c00651] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The contact system comprises a series of serine proteases that mediate procoagulant and proinflammatory activities via the intrinsic pathway of coagulation and the kallikrein-kinin system, respectively. Inhibition of Factor XIIa (FXIIa), an initiator of the contact system, has been demonstrated to lead to thrombo-protection and anti-inflammatory effects in animal models and serves as a potentially safer target for the development of antithrombotics. Herein, we describe the use of the Randomised Nonstandard Peptide Integrated Discovery (RaPID) mRNA display technology to identify a series of potent and selective cyclic peptide inhibitors of FXIIa. Cyclic peptides were evaluated in vitro, and three lead compounds exhibited significant prolongation of aPTT, a reduction in thrombin generation, and an inhibition of bradykinin formation. We also describe our efforts to identify the critical residues for binding FXIIa through alanine scanning, analogue generation, and via in silico methods to predict the binding mode of our lead cyclic peptide inhibitors.
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Affiliation(s)
- Daniel J Ford
- 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
| | - Nisharnthi M Duggan
- 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
| | - Sarah E Fry
- 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
| | - Jorge Ripoll-Rozada
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Stijn M Agten
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Wenyu Liu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Tokyo 113-0033, Japan
| | - Leo Corcilius
- 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
| | - Tilman M Hackeng
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Rene van Oerle
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Henri M H Spronk
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - 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, Sydney, New South Wales 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Vishnu Mini Sasi
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 0200, Australia.,Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Joe A Kaczmarski
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 0200, Australia.,Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Colin J Jackson
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 0200, Australia.,Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Toby Passioura
- 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.,Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Tokyo 113-0033, Japan.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Tokyo 113-0033, Japan
| | - 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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12
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Carle V, Wu Y, Mukherjee R, Kong XD, Rogg C, Laurent Q, Cecere E, Villequey C, Konakalla MS, Maric T, Lamers C, Díaz-Perlas C, Butler K, Goto J, Stegmayr B, Heinis C. Development of Selective FXIa Inhibitors Based on Cyclic Peptides and Their Application for Safe Anticoagulation. J Med Chem 2021; 64:6802-6813. [PMID: 33974422 DOI: 10.1021/acs.jmedchem.1c00056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Coagulation factor XI (FXI) has emerged as a promising target for the development of safer anticoagulation drugs that limit the risk of severe and life-threatening bleeding. Herein, we report the first cyclic peptide-based FXI inhibitor that selectively and potently inhibits activated FXI (FXIa) in human and animal blood. The cyclic peptide inhibitor (Ki = 2.8 ± 0.5 nM) achieved anticoagulation effects that are comparable to that of the gold standard heparin applied at a therapeutic dose (0.3-0.7 IU/mL in plasma) but with a substantially broader estimated therapeutic range. We extended the plasma half-life of the peptide via PEGylation and demonstrated effective FXIa inhibition over extended periods in vivo. We validated the anticoagulant effects of the PEGylated inhibitor in an ex vivo hemodialysis model with human blood. Our work shows that FXI can be selectively targeted with peptides and provides a promising candidate for the development of a safe anticoagulation therapy.
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Affiliation(s)
- Vanessa Carle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yuteng Wu
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Rakesh Mukherjee
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Chloé Rogg
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Quentin Laurent
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Enza Cecere
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Camille Villequey
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Madhuree S Konakalla
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tamara Maric
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christina Lamers
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kaycie Butler
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Junko Goto
- Department of Public Health and Clinical Medicine, University of Umeå, SE-901 87 Umeå, Sweden
| | - Bernd Stegmayr
- Department of Public Health and Clinical Medicine, University of Umeå, SE-901 87 Umeå, Sweden
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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13
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High-Throughput Docking and Molecular Dynamics Simulations towards the Identification of Potential Inhibitors against Human Coagulation Factor XIIa. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2020:2852051. [PMID: 32549905 PMCID: PMC7261338 DOI: 10.1155/2020/2852051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/22/2020] [Accepted: 04/07/2020] [Indexed: 11/17/2022]
Abstract
Human coagulation factor XIIa (FXIIa) is a trypsin-like serine protease that is involved in pathologic thrombosis. As a potential target for designing safe anticoagulants, FXIIa has received a great deal of interest in recent years. In the present study, we employed virtual high-throughput screening of 500,064 compounds within Enamine database to acquire the most potential inhibitors of FXIIa. Subsequently, 18 compounds with significant binding energy (from -65.195 to -15.726 kcal/mol) were selected, and their ADMET properties were predicted to select representative inhibitors. Three compounds (Z1225120358, Z432246974, and Z146790068) exhibited excellent binding affinity and druggability. MD simulation for FXIIa-ligand complexes was carried out to reveal the stability and inhibition mechanism of these three compounds. Through the inhibition of activated factor XIIa assay, we tested the activity of five compounds Z1225120358, Z432246974, Z45287215, Z30974175, and Z146790068, with pIC50 values of 9.3∗10−7, 3.0∗10−5, 7.8∗10−7, 8.7∗10−7, and 1.3∗10−6 M, respectively; the AMDET properties of Z45287215 and Z30974175 show not well but have better inhibition activity. We also found that compounds Z1225120358, Z45287215, Z30974175, and Z146790068 could be more inhibition of FXIIa than Z432246974. Collectively, compounds Z1225120358, Z45287215, Z30974175, and Z146790068 were anticipated to be promising drug candidates for inhibition of FXIIa.
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14
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Abstract
Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.
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15
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Naito N, Ukita R, Wilbs J, Wu K, Lin X, Carleton NM, Roberts K, Jiang S, Heinis C, Cook KE. Combination of polycarboxybetaine coating and factor XII inhibitor reduces clot formation while preserving normal tissue coagulation during extracorporeal life support. Biomaterials 2021; 272:120778. [PMID: 33812214 DOI: 10.1016/j.biomaterials.2021.120778] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/17/2022]
Abstract
Blood contact with high surface area medical devices, such as dialysis and extracorporeal life support (ECLS), induces rapid surface coagulation. Systemic anticoagulation, such as heparin, is thus necessary to slow clot formation, but some patients suffer from bleeding complications. Both problems might be reduced by 1) replacing heparin anticoagulation with artificial surface inhibition of the protein adsorption that initiates coagulation and 2) selective inhibition of the intrinsic branch of the coagulation cascade. This approach was evaluated by comparing clot formation and bleeding times during short-term ECLS using zwitterionic polycarboxybetaine (PCB) surface coatings combined with either a potent, selective, bicyclic peptide inhibitor of activated Factor XII (FXII900) or standard heparin anticoagulation. Rabbits underwent venovenous ECLS with small sham oxygenators for 60 min using three means of anticoagulation (n = 4 ea): (1) PCB coating + FXII900 infusion, (2) PCB coating + heparin infusion with an activated clotting time of 220-300s, and (3) heparin infusion alone. Sham oxygenator blood clot weights in the PCB + FXII900 and PCB + heparin groups were 4% and 25% of that in the heparin group (p < 10-6 and p < 10-5), respectively. At the same time, the bleeding time remained normal in the PCB + FXII900 group (2.4 ± 0.2 min) but increased to 4.8 ± 0.5 and 5.1 ± 0.7 min in the PCB + heparin and heparin alone groups (p < 10-4 and 0.01). Sham oxygenator blood flow resistance was significantly lower in the PCB + FXII900 and PCB + heparin groups than in the heparin only group (p < 10-6 and 10-5). These results were confirmed by gross and scanning electron microscopy (SEM) images and fibrinopeptide A (FPA) concentrations. Thus, the combined use of PCB coating and FXII900 markedly reduced sham oxygenator coagulation and tissue bleeding times versus the clinical standard of heparin anticoagulation and is a promising anticoagulation method for clinical ECLS.
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Affiliation(s)
- Noritsugu Naito
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rei Ukita
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonas Wilbs
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kan Wu
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Xiaojie Lin
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Neil M Carleton
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kalliope Roberts
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shaoyi Jiang
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Keith E Cook
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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16
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Peptide library screening as a tool to derive potent therapeutics: current approaches and future strategies. Future Med Chem 2020; 13:95-98. [PMID: 33275071 DOI: 10.4155/fmc-2020-0324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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17
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Structure-based design of small bicyclic peptide inhibitors of Cripto-1 activity. Biochem J 2020; 477:1391-1407. [PMID: 32215602 DOI: 10.1042/bcj20190953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/21/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
Bicyclic peptides assembled around small organic scaffolds are gaining an increasing interest as new potent, stable and highly selective therapeutics because of their uncommon ability to specifically recognize protein targets, of their small size that favor tissue penetration and of the versatility and easiness of the synthesis. We have here rationally designed bicyclic peptides assembled around a common tri-bromo-methylbenzene moiety in order to mimic the structure of the CFC domain of the oncogene Cripto-1 and, more specifically, to orient in the most fruitful way the hot spot residues H120 and W123. Through the CFC domain, Cripto-1 binds the ALK4 receptor and other protein partners supporting uncontrolled cell growth and proliferation. Soluble variants of CFC have the potential to inhibit these interactions suppressing the protein activity. A CFC analog named B3 binds ALK4 in vitro with an affinity in the nanomolar range. Structural analyses in solution via NMR and CD show that B3 has rather flexible conformations, like the parent CFC domain. The functional effects of B3 on the Cripto-1-positive NTERA cancer cell line have been evaluated showing that both CFC and B3 are cytotoxic for the cells and block the Cripto-1 intracellular signaling. Altogether, the data suggest that the administration of the soluble CFC and of the structurally related analog has the potential to inhibit tumor growth.
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18
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Factor XII/XIIa inhibitors: Their discovery, development, and potential indications. Eur J Med Chem 2020; 208:112753. [DOI: 10.1016/j.ejmech.2020.112753] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022]
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19
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McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
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20
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Korff M, Imberg L, Will JM, Bückreiß N, Kalinina SA, Wenzel BM, Kastner GA, Daniliuc CG, Barth M, Ovsepyan RA, Butov KR, Humpf HU, Lehr M, Panteleev MA, Poso A, Karst U, Steinmetzer T, Bendas G, Kalinin DV. Acylated 1H-1,2,4-Triazol-5-amines Targeting Human Coagulation Factor XIIa and Thrombin: Conventional and Microscale Synthesis, Anticoagulant Properties, and Mechanism of Action. J Med Chem 2020; 63:13159-13186. [DOI: 10.1021/acs.jmedchem.0c01635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marvin Korff
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Lukas Imberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Jonas M. Will
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149 Münster, Germany
| | - Nico Bückreiß
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Svetlana A. Kalinina
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149 Münster, Germany
| | - Benjamin M. Wenzel
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gregor A. Kastner
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Constantin G. Daniliuc
- Institute for Organic Chemistry, University of Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Maximilian Barth
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Ruzanna A. Ovsepyan
- Laboratory of Translational Medicine, Dmitriy Rogachev National Medical Research Center of Pediatric Hematology, Oncology, and Immunology, Samory Mashela str. 1, GSP-7, 117997 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 4 Kosygina St, 119991 Moscow, Russia
| | - Kirill R. Butov
- Laboratory of Translational Medicine, Dmitriy Rogachev National Medical Research Center of Pediatric Hematology, Oncology, and Immunology, Samory Mashela str. 1, GSP-7, 117997 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 4 Kosygina St, 119991 Moscow, Russia
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149 Münster, Germany
| | - Matthias Lehr
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Mikhail A. Panteleev
- Laboratory of Translational Medicine, Dmitriy Rogachev National Medical Research Center of Pediatric Hematology, Oncology, and Immunology, Samory Mashela str. 1, GSP-7, 117997 Moscow, Russia
- Faculty of Physics, Lomonosov Moscow State University, 1/2 Leninskie gory, 119991 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 4 Kosygina St, 119991 Moscow, Russia
- Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, 9 Institutskii per., 141700 Dolgoprudnyi, Russia
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
- Department of Internal Medicine VIII, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149 Münster, Germany
| | - Torsten Steinmetzer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerd Bendas
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Dmitrii V. Kalinin
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
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21
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Berlinck RGS, Bernardi DI, Fill T, Fernandes AAG, Jurberg ID. The chemistry and biology of guanidine secondary metabolites. Nat Prod Rep 2020; 38:586-667. [PMID: 33021301 DOI: 10.1039/d0np00051e] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2017-2019Guanidine natural products isolated from microorganisms, marine invertebrates and terrestrial plants, amphibians and spiders, represented by non-ribosomal peptides, guanidine-bearing polyketides, alkaloids, terpenoids and shikimic acid derived, are the subject of this review. The topics include the discovery of new metabolites, total synthesis of natural guanidine compounds, biological activity and mechanism-of-action, biosynthesis and ecological functions.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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22
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Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic β-amino acids. Nat Chem 2020; 12:1081-1088. [PMID: 32839601 DOI: 10.1038/s41557-020-0525-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/15/2020] [Indexed: 02/05/2023]
Abstract
Peptides that contain β-amino acids display stable secondary structures, such as helices and sheets, and are often referred to as foldamers. Cyclic β2,3-amino acids (cβAAs), such as 2-aminocyclohexanecarboxylic acid (2-ACHC), are strong helix/turn inducers due to their restricted conformations. Here we report the ribosomal synthesis of foldamer peptides that contain multiple, up to ten, consecutive cβAAs via genetic code reprogramming. We also report the de novo discovery of macrocyclic cβAA-containing peptides capable of binding to a protein target. As a demonstration, potent binders with low-to-subnanomolar KD values were identified for human factor XIIa (hFXIIa) and interferon-gamma receptor 1, from a library of their 1012 members. One of the anti-hFXIIa macrocyclic peptides that exhibited a high inhibitory activity and serum stability was co-crystallized with hFXIIa. The X-ray structure revealed that it adopts an antiparallel β-sheet structure induced by a (1S,2S)-2-ACHC residue via the formation of two γ-turns. This work demonstrates the potential of this platform to explore the previously inaccessible sequence space of cβAA-containing peptides.
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23
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Golubev P, Guranova N, Krasavin M. 1,3,5-Triazinanes as Formaldimine Surrogates in the Ugi Reaction. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Pavel Golubev
- Institute of Chemistry; Saint Petersburg State University; 26 Universitetsky prospect 198504 Peterhof Russia
| | - Natalia Guranova
- Institute of Chemistry; Saint Petersburg State University; 26 Universitetsky prospect 198504 Peterhof Russia
| | - Mikhail Krasavin
- Institute of Chemistry; Saint Petersburg State University; 26 Universitetsky prospect 198504 Peterhof Russia
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24
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Wilbs J, Kong XD, Middendorp SJ, Prince R, Cooke A, Demarest CT, Abdelhafez MM, Roberts K, Umei N, Gonschorek P, Lamers C, Deyle K, Rieben R, Cook KE, Angelillo-Scherrer A, Heinis C. Cyclic peptide FXII inhibitor provides safe anticoagulation in a thrombosis model and in artificial lungs. Nat Commun 2020; 11:3890. [PMID: 32753636 PMCID: PMC7403315 DOI: 10.1038/s41467-020-17648-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/08/2020] [Indexed: 01/06/2023] Open
Abstract
Inhibiting thrombosis without generating bleeding risks is a major challenge in medicine. A promising solution may be the inhibition of coagulation factor XII (FXII), because its knock-out or inhibition in animals reduced thrombosis without causing abnormal bleeding. Herein, we have engineered a macrocyclic peptide inhibitor of activated FXII (FXIIa) with sub-nanomolar activity (Ki = 370 ± 40 pM) and a high stability (t1/2 > 5 days in plasma), allowing for the preclinical evaluation of a first synthetic FXIIa inhibitor. This 1899 Da molecule, termed FXII900, efficiently blocks FXIIa in mice, rabbits, and pigs. We found that it reduces ferric-chloride-induced experimental thrombosis in mice and suppresses blood coagulation in an extracorporeal membrane oxygenation (ECMO) setting in rabbits, all without increasing the bleeding risk. This shows that FXIIa activity is controllable in vivo with a synthetic inhibitor, and that the inhibitor FXII900 is a promising candidate for safe thromboprotection in acute medical conditions.
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Affiliation(s)
- Jonas Wilbs
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Simon J Middendorp
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Raja Prince
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, CH-3010, Bern, Switzerland.,Department of Clinical Research, University of Bern, CH-3008, Bern, Switzerland
| | - Alida Cooke
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Caitlin T Demarest
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Mai M Abdelhafez
- Department of Clinical Research, University of Bern, CH-3008, Bern, Switzerland
| | - Kalliope Roberts
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Nao Umei
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Patrick Gonschorek
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christina Lamers
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Kaycie Deyle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Robert Rieben
- Department of Clinical Research, University of Bern, CH-3008, Bern, Switzerland
| | - Keith E Cook
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Anne Angelillo-Scherrer
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, CH-3010, Bern, Switzerland.,Department of Clinical Research, University of Bern, CH-3008, Bern, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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25
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Abstract
Macrocyclic peptides make up an emerging class of candidate therapeutics and chemical probes, with properties that make them potentially applicable to a wide range of targets that are intractable using current pharmacological agents. Additionally, a number of biochemical screening strategies have been developed, particularly over the past decade, that allow for the massively parallel screening of cyclic peptide libraries of up to 1 trillion compounds or more, leading to the isolation of molecules with exceptional target affinity, selectivity, and bioactivity. Clinical development of compounds derived from such screens is already underway, but the nature of these molecules means that such development is likely to follow pathways different from those of traditional small molecule drugs or well-established biologics such as monoclonal antibodies. In addition, recent work has shown that the biochemical techniques used to identify macrocyclic peptides can also be used to rapidly characterize and optimize them. These findings are likely to facilitate the development of these compounds as chemical probes and as therapeutics for areas of unmet medical need.
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Affiliation(s)
- Toby Passioura
- Sydney Analytical, School of Life and Environmental Sciences and School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
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26
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Peng B, Xue G, Xu D, Feng Z, Chen J, Huang M, Lu H, Gong L. Expression and purification of recombinant serine protease domain of human coagulation factor XII in Pichia pastoris. Biosci Biotechnol Biochem 2019; 83:1815-1821. [DOI: 10.1080/09168451.2019.1621151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
ABSTRACT
Human coagulation factor XII, the initiating factor in the intrinsic coagulation pathway, is critical for pathological thrombosis but not for hemostasis. Pharmacologic inhibition of factor XII is an attractive alternative in providing protection from pathologic thrombus formation while minimizing hemorrhagic risk. Large quantity of recombinant active factor XII is required for screening inhibitors and further research. In the present study, we designed and expressed the recombinant serine protease domain of factor XII in Pichia pastoris strain X-33, which is a eukaryotic expression model organism with low cost. The purification protocol was simplified and the protein yield was high (~20 mg/L medium). The purified serine protease domain of factor XII behaved homogeneously as a monomer, exhibited comparable activity with the human βFXIIa, and accelerated clot formation in human plasma. This study provides the groundwork for factor XII inhibitors screening and further research.
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Affiliation(s)
- Bangya Peng
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | - Guangpu Xue
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Dongfang Xu
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | - Zanjie Feng
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | - Jing Chen
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | | | - Hongling Lu
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | - Lihu Gong
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
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Ukita R, Wu K, Lin X, Carleton NM, Naito N, Lai A, Do-Nguyen CC, Demarest CT, Jiang S, Cook KE. Zwitterionic poly-carboxybetaine coating reduces artificial lung thrombosis in sheep and rabbits. Acta Biomater 2019; 92:71-81. [PMID: 31082571 PMCID: PMC6633914 DOI: 10.1016/j.actbio.2019.05.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 12/24/2022]
Abstract
Current artificial lungs fail in 1-4 weeks due to surface-induced thrombosis. Biomaterial coatings may be applied to anticoagulate artificial surfaces, but none have shown marked long-term effectiveness. Poly-carboxybetaine (pCB) coatings have shown promising results in reducing protein and platelet-fouling in vitro. However, in vivo hemocompatibility remains to be investigated. Thus, three different pCB-grafting approaches to artificial lung surfaces were first investigated: 1) graft-to approach using 3,4-dihydroxyphenylalanine (DOPA) conjugated with pCB (DOPA-pCB); 2) graft-from approach using the Activators ReGenerated by Electron Transfer method of atom transfer radical polymerization (ARGET-ATRP); and 3) graft-to approach using pCB randomly copolymerized with hydrophobic moieties. One device coated with each of these methods and one uncoated device were attached in parallel within a veno-venous sheep extracorporeal circuit with no continuous anticoagulation (N = 5 circuits). The DOPA-pCB approach showed the least increase in blood flow resistance and the lowest incidence of device failure over 36-hours. Next, we further investigated the impact of tip-to-tip DOPA-pCB coating in a 4-hour rabbit study with veno-venous micro-artificial lung circuit at a higher activated clotting time of 220-300 s (N ≥ 5). Here, DOPA-pCB reduced fibrin formation (p = 0.06) and gross thrombus formation by 59% (p < 0.05). Therefore, DOPA-pCB is a promising material for improving the anticoagulation of artificial lungs. STATEMENT OF SIGNIFICANCE: Chronic lung diseases lead to 168,000 deaths each year in America, but only 2300 lung transplantations happen each year. Hollow fiber membrane oxygenators are clinically used as artificial lungs to provide respiratory support for patients, but their long-term viability is hindered by surface-induced clot formation that leads to premature device failure. Among different coatings investigated for blood-contacting applications, poly-carboxybetaine (pCB) coatings have shown remarkable reduction in protein adsorption in vitro. However, their efficacy in vivo remains unclear. This is the first work that investigates various pCB-coating methods on artificial lung surfaces and their biocompatibility in sheep and rabbit studies. This work highlights the promise of applying pCB coatings on artificial lungs to extend its durability and enable long-term respiratory support for lung disease patients.
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Affiliation(s)
- Rei Ukita
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA.
| | - Kan Wu
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195-1750, USA
| | - Xiaojie Lin
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195-1750, USA
| | - Neil M Carleton
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA
| | - Noritsugu Naito
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA
| | - Angela Lai
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA
| | - Chi Chi Do-Nguyen
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA
| | - Caitlin T Demarest
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA
| | - Shaoyi Jiang
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195-1750, USA
| | - Keith E Cook
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Scott Hall 4(th) Floor, Pittsburgh, PA 15213, USA
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Pathak M, Manna R, Li C, Kaira BG, Hamad BK, Belviso BD, Bonturi CR, Dreveny I, Fischer PM, Dekker LV, Oliva MLV, Emsley J. Crystal structures of the recombinant β-factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:578-591. [DOI: 10.1107/s2059798319006910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 11/10/2022]
Abstract
Coagulation factor XII (FXII) is a key initiator of the contact pathway, which contributes to inflammatory pathways. FXII circulates as a zymogen, which when auto-activated forms factor XIIa (FXIIa). Here, the production of the recombinant FXIIa protease domain (βFXIIaHis) with yields of ∼1–2 mg per litre of insect-cell culture is reported. A second construct utilized an N-terminal maltose-binding protein (MBP) fusion (MBP-βFXIIaHis). Crystal structures were determined of MBP-βFXIIaHisin complex with the inhibitor D-Phe-Pro-Arg chloromethyl ketone (PPACK) and of βFXIIaHisin isolation. The βFXIIaHisstructure revealed that the S2 and S1 pockets were occupied by Thr and Arg residues, respectively, from an adjacent molecule in the crystal. The Thr-Arg sequence mimics the P2–P1 FXIIa cleavage-site residues present in the natural substrates prekallikrein and FXII, and Pro-Arg (from PPACK) mimics the factor XI cleavage site. A comparison of the βFXIIaHisstructure with the available crystal structure of the zymogen-like FXII protease revealed large conformational changes centred around the S1 pocket and an alternate conformation for the 99-loop, Tyr99 and the S2 pocket. Further comparison with activated protease structures of factors IXa and Xa, which also have the Tyr99 residue, reveals that a more open form of the S2 pocket only occurs in the presence of a substrate mimetic. The FXIIa inhibitors EcTI and infestin-4 have Pro-Arg and Phe-Arg P2–P1 sequences, respectively, and the interactions that these inhibitors make with βFXIIa are also described. These structural studies of βFXIIa provide insight into substrate and inhibitor recognition and establish a scaffold for the structure-guided drug design of novel antithrombotic and anti-inflammatory agents.
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An anticoagulant peptide from Porphyra yezoensis inhibits the activity of factor XIIa: In vitro and in silico analysis. J Mol Graph Model 2019; 89:225-233. [DOI: 10.1016/j.jmgm.2019.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 11/30/2022]
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Ottl J, Leder L, Schaefer JV, Dumelin CE. Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery. Molecules 2019; 24:E1629. [PMID: 31027189 PMCID: PMC6514559 DOI: 10.3390/molecules24081629] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 01/22/2023] Open
Abstract
The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.
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Affiliation(s)
- Johannes Ottl
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Lukas Leder
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Jonas V Schaefer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
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31
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 412] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
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32
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Asciutto EK, Kopanchuk S, Lepland A, Simón-Gracia L, Aleman C, Teesalu T, Scodeller P. Phage-Display-Derived Peptide Binds to Human CD206 and Modeling Reveals a New Binding Site on the Receptor. J Phys Chem B 2019; 123:1973-1982. [DOI: 10.1021/acs.jpcb.8b11876] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eliana K. Asciutto
- School of Science and Technology, National University of San Martin (UNSAM) and CONICET, Campus Migueletes, 25 de Mayo y Francia, CP 1650 San Martín, Buenos Aires, Argentina
| | - Sergei Kopanchuk
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Anni Lepland
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 14B, Tartu 50411, Estonia
| | - Lorena Simón-Gracia
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 14B, Tartu 50411, Estonia
| | - Carlos Aleman
- Departament d’Enginyeria Química and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Tambet Teesalu
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 14B, Tartu 50411, Estonia
- Cancer Research Center, Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
- Center for Nanomedicine and Department of Cell, Molecular and Developmental Biology, University of California, Santa Barbara Santa Barbara, California 93106, United States
| | - Pablo Scodeller
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 14B, Tartu 50411, Estonia
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Eder M, Pavan S, Bauder-Wüst U, van Rietschoten K, Baranski AC, Harrison H, Campbell S, Stace CL, Walker EH, Chen L, Bennett G, Mudd G, Schierbaum U, Leotta K, Haberkorn U, Kopka K, Teufel DP. Bicyclic Peptides as a New Modality for Imaging and Targeting of Proteins Overexpressed by Tumors. Cancer Res 2019; 79:841-852. [DOI: 10.1158/0008-5472.can-18-0238] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 10/11/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022]
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34
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Richelle GJJ, Schmidt M, Ippel H, Hackeng TM, van Maarseveen JH, Nuijens T, Timmerman P. A One-Pot "Triple-C" Multicyclization Methodology for the Synthesis of Highly Constrained Isomerically Pure Tetracyclic Peptides. Chembiochem 2018; 19:1934-1938. [PMID: 29944773 DOI: 10.1002/cbic.201800346] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/24/2022]
Abstract
A broadly applicable one-pot methodology for the facile transformation of linear peptides into tetracyclic peptides through a chemoenzymatic peptide synthesis/chemical ligation of peptides onto scaffolds/copper(I)-catalyzed reaction (CEPS/CLIPS/CuAAC; "triple-C") locking methodology is reported. Linear peptides with varying lengths (≥14 amino acids), comprising two cysteines and two azidohomoalanines (Aha), were efficiently cyclized head-to-tail by using the peptiligase variant omniligase-1 (CEPS). Subsequent ligation-cyclization with tetravalent (T41/2 ) scaffolds containing two bromomethyl groups (CLIPS) and two alkyne functionalities (CuAAC) yielded isomerically pure tetracyclic peptides. Sixteen different functional tetracycles, derived from bicyclic inhibitors against urokinase plasminogen activator (uPA) and coagulation factor XIIa (FXIIa), were successfully synthesized and their bioactivities evaluated. Two of these (FF-T41/2 ) exhibited increased inhibitory activity against FXIIa, compared with a bicyclic control peptide. The corresponding hetero-bifunctional variants (UF/FU-T41/2 ), with a single copy of each inhibitory sequence, exhibited micromolar activities against both uPA and FXIIa; thus illustrating the potential of the "bifunctional tetracyclic peptide" inhibitor concept.
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Affiliation(s)
- Gaston J J Richelle
- Van 't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Marcel Schmidt
- Van 't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Enzypep B.V., Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
| | - Hans Ippel
- Department of Biochemistry, CARIM), Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Tilman M Hackeng
- Department of Biochemistry, CARIM), Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Timo Nuijens
- Enzypep B.V., Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
| | - Peter Timmerman
- Van 't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Pepscan Therapeutics, Zuidersluisweg 2, 8243 RC, Lelystad, The Netherlands
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35
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Huhmann S, Koksch B. Fine-Tuning the Proteolytic Stability of Peptides with Fluorinated Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800803] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Susanne Huhmann
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
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36
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Teufel DP, Bennett G, Harrison H, van Rietschoten K, Pavan S, Stace C, Le Floch F, Van Bergen T, Vermassen E, Barbeaux P, Hu TT, Feyen JHM, Vanhove M. Stable and Long-Lasting, Novel Bicyclic Peptide Plasma Kallikrein Inhibitors for the Treatment of Diabetic Macular Edema. J Med Chem 2018. [DOI: 10.1021/acs.jmedchem.7b01625] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniel P. Teufel
- Bicycle Therapeutics
Limited, Building 900, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Gavin Bennett
- Bicycle Therapeutics
Limited, Building 900, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Helen Harrison
- Bicycle Therapeutics
Limited, Building 900, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | | | - Silvia Pavan
- Bicycle Therapeutics
Limited, Building 900, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Catherine Stace
- Bicycle Therapeutics
Limited, Building 900, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | | | - Tine Van Bergen
- Thrombogenics
N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Elke Vermassen
- Thrombogenics
N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | | | - Tjing-Tjing Hu
- Thrombogenics
N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | | | - Marc Vanhove
- Thrombogenics
N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
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37
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Fischer PM. Design of Small-Molecule Active-Site Inhibitors of the S1A Family Proteases as Procoagulant and Anticoagulant Drugs. J Med Chem 2017; 61:3799-3822. [DOI: 10.1021/acs.jmedchem.7b00772] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter M. Fischer
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
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38
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Davis AM, Plowright AT, Valeur E. Directing evolution: the next revolution in drug discovery? Nat Rev Drug Discov 2017; 16:681-698. [PMID: 28935911 DOI: 10.1038/nrd.2017.146] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The strong biological rationale to pursue challenging drug targets such as protein-protein interactions has stimulated the development of novel screening strategies, such as DNA-encoded libraries, to allow broader areas of chemical space to be searched. There has also been renewed interest in screening natural products, which are the result of evolutionary selection for a function, such as interference with a key signalling pathway of a competing organism. However, recent advances in several areas, such as understanding of the biosynthetic pathways for natural products, synthetic biology and the development of biosensors to detect target molecules, are now providing new opportunities to directly harness evolutionary pressure to identify and optimize compounds with desired bioactivities. Here, we describe innovations in the key components of such strategies and highlight pioneering examples that indicate the potential of the directed-evolution concept. We also discuss the scientific gaps and challenges that remain to be addressed to realize this potential more broadly in drug discovery.
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Affiliation(s)
- Andrew M Davis
- AstraZeneca R&D Gothenburg, Pepparedsleden 1, Mölndal, 43150, Sweden
| | - Alleyn T Plowright
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Eric Valeur
- AstraZeneca R&D Gothenburg, Pepparedsleden 1, Mölndal, 43150, Sweden
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39
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Bouckaert C, Zhu S, Govers-Riemslag JW, Depoorter M, Diamond SL, Pochet L. Discovery and assessment of water soluble coumarins as inhibitors of the coagulation contact pathway. Thromb Res 2017; 157:126-133. [DOI: 10.1016/j.thromres.2017.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/26/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022]
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40
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Deyle K, Kong XD, Heinis C. Phage Selection of Cyclic Peptides for Application in Research and Drug Development. Acc Chem Res 2017; 50:1866-1874. [PMID: 28719188 DOI: 10.1021/acs.accounts.7b00184] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclic peptides can bind to protein targets with high affinities and selectivities, which makes them an attractive modality for the development of research reagents and therapeutics. Additional properties, including low inherent toxicity, efficient chemical synthesis, and facile modification with labels or immobilization reagents, increase their attractiveness. Cyclic peptide ligands against a wide range of protein targets have been isolated from natural sources such as bacteria, fungi, plants, and animals. Many of them are currently used as research tools, and several have found application as therapeutics, such as the peptide hormones oxytocin and vasopressin and the antibiotics vancomycin and daptomycin, proving the utility of cyclic peptides in research and medicine. With the advent of phage display and other in vitro evolution techniques, it has become possible to generate cyclic peptide binders to diverse protein targets for which no natural peptides have been discovered. A highly robust and widely applied approach is based on the cyclization of peptides displayed on phage via a disulfide bridge. Disulfide-cyclized peptide ligands to more than a hundred different proteins have been reported in the literature. Technology advances achieved over the last three decades, including methods for generating larger phage display libraries, improved phage panning protocols, new cyclic peptide formats, and high-throughput sequencing, have enabled the generation of cyclic peptides with ever better binding affinities to more challenging targets. A relatively new cyclic peptide format developed using phage display involves bicyclic peptides. These molecules consist of two macrocyclic peptide rings cyclized through a chemical linker. Compared to monocyclic peptides of comparable molecular mass, bicyclic peptides are more constrained in their conformation. As a result, they can bind to their targets with a higher affinity and are more resistant to proteolytic degradation. Phage-encoded bicyclic peptides are generated by chemically cyclizing random peptide libraries on phage. Binders are identified by conventional phage panning and DNA sequencing. Next-generation sequencing and new sequence alignment tools have enabled the rapid identification of bicyclic peptides. Bicyclic peptide ligands were developed against a range of diverse target classes including enzymes, receptors, and cytokines. Most ligands bind with nanomolar affinities, with some reaching the picomolar range. To date, several bicyclic peptides have been positively evaluated in preclinical studies, and the first clinical tests are in sight. While bicyclic peptide phage display was developed with therapeutic applications in mind, these peptides are increasingly used as research tools for target evaluation or as basic research probes as well. Given the efficient development method, the ease of synthesis and handling, and the favorable binding and biophysical properties, bicyclic peptides are being developed against more and more targets, ever increasing their potential applications in research and medicine.
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Affiliation(s)
- Kaycie Deyle
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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41
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Rhodes CA, Pei D. Bicyclic Peptides as Next-Generation Therapeutics. Chemistry 2017; 23:12690-12703. [PMID: 28590540 DOI: 10.1002/chem.201702117] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Indexed: 12/21/2022]
Abstract
Bicyclic peptides have greater conformational rigidity and metabolic stability than linear and monocyclic peptides and are capable of binding to challenging drug targets with antibody-like affinity and specificity. Powerful combinatorial library technologies have recently been developed to rapidly synthesize and screen large bicyclic peptide libraries for ligands against enzymes, receptors, and protein-protein interaction targets. Bicyclic peptides have been developed as potential therapeutics against a wide range of diseases, drug targeting agents, imaging/diagnostic probes, and research tools. In this Minireview, we provide a summary of the recent progresses on the synthesis and applications of bicyclic peptides.
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Affiliation(s)
- Curran A Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210, USA
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42
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The plasma contact system, a protease cascade at the nexus of inflammation, coagulation and immunity. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2118-2127. [PMID: 28743596 DOI: 10.1016/j.bbamcr.2017.07.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 01/11/2023]
Abstract
The contact system is a potent procoagulant and proinflammatory plasma protease cascade that is initiated by binding ("contact")-induced, auto-activation of factor XII zymogen. Formed active serine protease FXIIa then cleaves plasma prekallikrein to kallikrein that in turn liberates the mediator bradykinin from its precursor high molecular weight kininogen. Bradykinin induces inflammation with implications for host defense and innate immunity. FXIIa also triggers the intrinsic pathway of coagulation that has been shown to critically contribute to thrombosis. Vice versa, FXII deficiency impairs thrombosis in animal models without inducing abnormal excessive bleeding. Recent work has established the FXIIa-driven contact system as promising target for anticoagulant and anti-inflammatory drugs. This review focuses on the biochemistry of the contact system, its regulation by endogenous and exogenous inhibitors, and roles in disease states. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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43
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Acylated heptapeptide binds albumin with high affinity and application as tag furnishes long-acting peptides. Nat Commun 2017; 8:16092. [PMID: 28714475 PMCID: PMC5520048 DOI: 10.1038/ncomms16092] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/24/2017] [Indexed: 12/12/2022] Open
Abstract
The rapid renal clearance of peptides in vivo limits this attractive platform for the treatment of a broad range of diseases that require prolonged drug half-lives. An intriguing approach for extending peptide circulation times works through a ‘piggy-back’ strategy in which peptides bind via a ligand to the long-lived serum protein albumin. In accordance with this strategy, we developed an easily synthesized albumin-binding ligand based on a peptide-fatty acid chimera that has a high affinity for human albumin (Kd=39 nM). This ligand prolongs the elimination half-life of cyclic peptides in rats 25-fold to over seven hours. Conjugation to a peptide factor XII inhibitor developed for anti-thrombotic therapy extends the half-life from 13 minutes to over five hours, inhibiting coagulation for eight hours in rabbits. This high-affinity albumin ligand could potentially extend the half-life of peptides in human to several days, substantially broadening the application range of peptides as therapeutics. A major challenge for the application of peptide therapeutics is their short half-life in vivo. Here, the authors design peptide-fatty acid chimeras bearing an engineered linker that promotes albumin binding and allows longer circulation times of therapeutic peptides in animal models.
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