1
|
Dockerill M, Ford DJ, Angerani S, Alwis I, Dowman LJ, Ripoll-Rozada J, Smythe RE, Liu JST, Pereira PJB, Jackson SP, Payne RJ, Winssinger N. Development of supramolecular anticoagulants with on-demand reversibility. Nat Biotechnol 2024:10.1038/s41587-024-02209-z. [PMID: 38689027 DOI: 10.1038/s41587-024-02209-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/14/2024] [Indexed: 05/02/2024]
Abstract
Drugs are administered at a dosing schedule set by their therapeutic index, and termination of action is achieved by clearance and metabolism of the drug. In some cases, such as anticoagulant drugs or immunotherapeutics, it is important to be able to quickly reverse the drug's action. Here, we report a general strategy to achieve on-demand reversibility by designing a supramolecular drug (a noncovalent assembly of two cooperatively interacting drug fragments held together by transient hybridization of peptide nucleic acid (PNA)) that can be reversed with a PNA antidote that outcompetes the hybridization between the fragments. We demonstrate the approach with thrombin-inhibiting anticoagulants, creating very potent and reversible bivalent direct thrombin inhibitors (Ki = 74 pM). The supramolecular inhibitor effectively inhibited thrombus formation in mice in a needle injury thrombosis model, and this activity could be reversed by administration of the PNA antidote. This design is applicable to therapeutic targets where two binding sites can be identified.
Collapse
Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Daniel J Ford
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Imala Alwis
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Jorge Ripoll-Rozada
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Rhyll E Smythe
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Joanna S T Liu
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Shaun P Jackson
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
2
|
Maxwell JWC, Hawkins PME, Watson EE, Payne RJ. Exploiting Chemical Protein Synthesis to Study the Role of Tyrosine Sulfation on Anticoagulants from Hematophagous Organisms. Acc Chem Res 2023; 56:2688-2699. [PMID: 37708351 DOI: 10.1021/acs.accounts.3c00388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Tyrosine sulfation is a post-translational modification (PTM) that modulates function by mediating key protein-protein interactions. One of the early proteins shown to possess this PTM was hirudin, produced in the salivary glands of the medicinal leech Hirudo medicinalis, whereby tyrosine sulfation led to a ∼10-fold improvement in α-thrombin inhibitory activity. Outside of this pioneering discovery, the involvement of tyrosine sulfation in modulating the activity of salivary proteins from other hematophagous organisms was unknown. We hypothesized that the intrinsic instability of the tyrosine sulfate functionality, particularly under the acidic conditions used to isolate and analyze peptides and proteins, has led to poor detection during the isolation and/or expression of these molecules.Herein, we summarize our efforts to interrogate the functional role of tyrosine sulfation in the thrombin inhibitory and anticoagulant activity of salivary peptides and proteins from a range of different blood feeding organisms, including leeches, ticks, mosquitoes, and flies. Specifically, we have harnessed synthetic chemistry to efficiently generate homogeneously sulfated peptides and proteins for detailed structure-function studies both in vitro and in vivo.Our studies began with the leech protein hirudin P6 (from Hirudinaria manillensis), which is both sulfated on tyrosine and O-glycosylated at a nearby threonine residue. Synthetically, this was achieved through solid-phase peptide synthesis (SPPS) with a late-stage on-resin sulfation, followed by native chemical ligation and a folding step to generate six differentially modified variants of hirudin P6 to assess the functional interplay between O-glycosylation and tyrosine sulfation. A one-pot, kinetically controlled ligation of three peptide fragments was used to assemble homogeneously sulfoforms of madanin-1 and chimadanin from the tick Haemaphysalis longicornis. Dual tyrosine sulfation at two distinct sites was shown to increase the thrombin inhibitory activity by up to 3 orders of magnitude through a novel interaction with exosite II of thrombin. The diselenide-selenoester ligation developed by our lab provided us with a means to rapidly assemble a library of different sulfated tick anticoagulant proteins: the andersonins, hyalomins, madanin-like proteins, and hemeathrins, thus enabling the generation of key structure-activity data on this family of proteins. We have also confirmed the presence of tyrosine sulfation in the anticoagulant proteins of Anopheles mosquitoes (anophelins) and the Tsetse fly (TTI) via insect expression and mass spectrometric analysis. These molecules were subsequently synthesized and assessed for thrombin inhibitory and anticoagulant activity. Activity was significantly improved by the addition of tyrosine sulfate modifications and led to molecules with potent antithrombotic activity in an in vivo murine thrombosis model.The Account concludes with our most recent work on the design of trivalent hybrids that tandemly occupy the active site and both exosites (I and II) of α-thrombin, with a TTI-anophelin hybrid (Ki = 20 fM against α-thrombin) being one of the most potent protease inhibitors and anticoagulants ever generated. Taken together, this Account highlights the importance of the tyrosine sulfate post-translational modification within salivary proteins from blood feeding organisms for enhancing anticoagulant activity. This work lays the foundation for exploiting native or engineered variants as therapeutic leads for thrombotic disorders in the future.
Collapse
Affiliation(s)
- Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Sydney, NSW 2006, Australia
| | - Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Sydney, NSW 2006, Australia
| | - Emma E Watson
- School of Chemistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Sydney, NSW 2006, Australia
| |
Collapse
|
3
|
Liu C, Liu X, Zhou M, Xia C, Lyu Y, Peng Q, Soni C, Zhou Z, Su Q, Wu Y, Weerapana E, Gao J, Chatterjee A, Cheng L, Jia N. Fluorosulfate as a Latent Sulfate in Peptides and Proteins. J Am Chem Soc 2023; 145:20189-20195. [PMID: 37647087 PMCID: PMC10623540 DOI: 10.1021/jacs.3c07937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Sulfation widely exists in the eukaryotic proteome. However, understanding the biological functions of sulfation in peptides and proteins has been hampered by the lack of methods to control its spatial or temporal distribution in the proteome. Herein, we report that fluorosulfate can serve as a latent precursor of sulfate in peptides and proteins, which can be efficiently converted to sulfate by hydroxamic acid reagents under physiologically relevant conditions. Photocaging the hydroxamic acid reagents further allowed for the light-controlled activation of functional sulfopeptides. This work provides a valuable tool for probing the functional roles of sulfation in peptides and proteins.
Collapse
Affiliation(s)
- Chao Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Xueyi Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Mi Zhou
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chaoshuang Xia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Yuhan Lyu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Qianni Peng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chintan Soni
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Zefeng Zhou
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Qiwen Su
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yujia Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Lin Cheng
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Niu Jia
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
4
|
Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
Collapse
Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
5
|
Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
Collapse
Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| |
Collapse
|
6
|
Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
Collapse
Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
| |
Collapse
|
7
|
Bedding MJ, Kulkarni SS, Payne RJ. Diselenide-selenoester ligation in the chemical synthesis of proteins. Methods Enzymol 2022; 662:363-399. [PMID: 35101218 DOI: 10.1016/bs.mie.2021.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Peptides and proteins represent an important class of biomolecules responsible for a plethora of structural and functional roles in vivo. Following their translation on the ribosome, the majority of eukaryotic proteins are post-translationally modified, leading to a proteome that is much larger than the number of genes present in a given organism. In order to understand the functional role of a given protein modification, it is necessary to access peptides and proteins bearing homogeneous and site-specific modifications. Accordingly, there has been significant research effort centered on the development of peptide ligation methodologies for the chemical synthesis of modified proteins. In this chapter we outline the discovery and development of a contemporary methodology called the diselenide-selenoester ligation (DSL) that enables the rapid and efficient fusion of peptide fragments to generate synthetic proteins. The practical aspects of using DSL for the preparation of chemically modified peptides and proteins in the laboratory is described. In addition, recent advances in the application of the methodology are outlined, exemplified by the synthesis and biological evaluation of a number of complex protein targets.
Collapse
Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia
| | - Sameer S Kulkarni
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia.
| |
Collapse
|
8
|
Tyrosine-O-sulfation is a widespread affinity enhancer among thrombin interactors. Biochem Soc Trans 2022; 50:387-401. [PMID: 34994377 DOI: 10.1042/bst20210600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/24/2022]
Abstract
Tyrosine-O-sulfation is a common post-translational modification (PTM) of proteins following the cellular secretory pathway. First described in human fibrinogen, tyrosine-O-sulfation has long been associated with the modulation of protein-protein interactions in several physiological processes. A number of relevant interactions for hemostasis are largely dictated by this PTM, many of which involving the serine proteinase thrombin (FIIa), a central player in the blood-clotting cascade. Tyrosine sulfation is not limited to endogenous FIIa ligands and has also been found in hirudin, a well-known and potent thrombin inhibitor from the medicinal leech, Hirudo medicinalis. The discovery of hirudin led to successful clinical application of analogs of leech-inspired molecules, but also unveiled several other natural thrombin-directed anticoagulant molecules, many of which undergo tyrosine-O-sulfation. The presence of this PTM has been shown to enhance the anticoagulant properties of these peptides from a range of blood-feeding organisms, including ticks, mosquitos and flies. Interestingly, some of these molecules display mechanisms of action that mimic those of thrombin's bona fide substrates.
Collapse
|
9
|
Koh CY, Shih N, Yip CYC, Li AWL, Chen W, Amran FS, Leong EJE, Iyer JK, Croft G, Mazlan MIB, Chee YL, Yap ES, Monroe DM, Hoffman M, Becker RC, de Kleijn DPV, Verma V, Gupta A, Chaudhary VK, Richards AM, Kini RM, Chan MY. Efficacy and safety of next-generation tick transcriptome-derived direct thrombin inhibitors. Nat Commun 2021; 12:6912. [PMID: 34824278 PMCID: PMC8617063 DOI: 10.1038/s41467-021-27275-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/28/2021] [Indexed: 01/18/2023] Open
Abstract
Despite their limitations, unfractionated heparin (UFH) and bivalirudin remain standard-of-care parenteral anticoagulants for percutaneous coronary intervention (PCI). We discovered novel direct thrombin inhibitors (DTIs) from tick salivary transcriptomes and optimised their pharmacologic activity. The most potent, ultravariegin, inhibits thrombin with a Ki of 4.0 pM, 445-fold better than bivalirudin. Unexpectedly, despite their greater antithrombotic effect, variegin/ultravariegin demonstrated less bleeding, achieving a 3-to-7-fold wider therapeutic index in rodent thrombosis and bleeding models. When used in combination with aspirin and ticagrelor in a porcine model, variegin/ultravariegin reduced stent thrombosis compared with antiplatelet therapy alone but achieved a 5-to-7-fold lower bleeding time than UFH/bivalirudin. Moreover, two antibodies screened from a naïve human antibody library effectively reversed the anticoagulant activity of ultravariegin, demonstrating proof-of-principle for antidote reversal. Variegin and ultravariegin are promising translational candidates for next-generation DTIs that may reduce peri-PCI bleeding in the presence of antiplatelet therapy.
Collapse
Affiliation(s)
- Cho Yeow Koh
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Norrapat Shih
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christina Y. C. Yip
- grid.412106.00000 0004 0621 9599Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Aaron Wei Liang Li
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Weiming Chen
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fathiah S. Amran
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Esther Jia En Leong
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Janaki Krishnamoorthy Iyer
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Grace Croft
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Muhammad Ibrahim Bin Mazlan
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yen-Lin Chee
- Department of Haematology, National Cancer Institute, Singapore, Singapore
| | - Eng-Soo Yap
- Department of Haematology, National Cancer Institute, Singapore, Singapore
| | - Dougald M. Monroe
- grid.10698.360000000122483208Division of Hematology/Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Maureane Hoffman
- grid.26009.3d0000 0004 1936 7961Department of Pathology, Duke University, Durham, NC USA
| | - Richard C. Becker
- grid.24827.3b0000 0001 2179 9593University of Cincinnati, Cincinnati, OH USA
| | - Dominique P. V. de Kleijn
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.7692.a0000000090126352Department of Vascular Surgery, University Medical Center Utrecht & Netherlands heart Institute, Utrecht, The Netherlands
| | - Vaishali Verma
- grid.8195.50000 0001 2109 4999Centre for Innovation in Infectious Disease Research, Education, and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Amita Gupta
- grid.8195.50000 0001 2109 4999Centre for Innovation in Infectious Disease Research, Education, and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Vijay K. Chaudhary
- grid.8195.50000 0001 2109 4999Centre for Innovation in Infectious Disease Research, Education, and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - A. Mark Richards
- grid.410759.e0000 0004 0451 6143Cardiovascular Research Institute, NUHS, Singapore, Singapore ,grid.29980.3a0000 0004 1936 7830Christchurch Heart Institute, University of Otago, Otago, New Zealand
| | - R. Manjunatha Kini
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Pharmacology, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mark Y. Chan
- grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.488497.e0000 0004 1799 3088Cardiac Department, National University Heart Centre, Singapore, Singapore
| |
Collapse
|
10
|
Lu S, Tirloni L, Oliveira MB, Bosio CF, Nardone GA, Zhang Y, Hinnebusch BJ, Ribeiro JM, Andersen JF. Identification of a substrate-like cleavage-resistant thrombin inhibitor from the saliva of the flea Xenopsylla cheopis. J Biol Chem 2021; 297:101322. [PMID: 34688666 PMCID: PMC8573170 DOI: 10.1016/j.jbc.2021.101322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
The salivary glands of the flea Xenopsylla cheopis, a vector of the plague bacterium, Yersinia pestis, express proteins and peptides thought to target the hemostatic and inflammatory systems of its mammalian hosts. Past transcriptomic analyses of salivary gland tissue revealed the presence of two similar peptides (XC-42 and XC-43) having no extensive similarities to any other deposited sequences. Here we show that these peptides specifically inhibit coagulation of plasma and the amidolytic activity of α-thrombin. XC-43, the smaller of the two peptides, is a fast, tight-binding inhibitor of thrombin with a dissociation constant of less than 10 pM. XC-42 exhibits similar selectivity as well as kinetic and binding properties. The crystal structure of XC-43 in complex with thrombin shows that despite its substrate-like binding mode, XC-43 is not detectably cleaved by thrombin and that it interacts with the thrombin surface from the enzyme catalytic site through the fibrinogen-binding exosite I. The low rate of hydrolysis was verified in solution experiments with XC-43, which show the substrate to be largely intact after 2 h of incubation with thrombin at 37 °C. The low rate of XC-43 cleavage by thrombin may be attributable to specific changes in the catalytic triad observable in the crystal structure of the complex or to extensive interactions in the prime sites that may stabilize the binding of cleavage products. Based on the increased arterial occlusion time, tail bleeding time, and blood coagulation parameters in rat models of thrombosis XC-43 could be valuable as an anticoagulant.
Collapse
Affiliation(s)
- Stephen Lu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Lucas Tirloni
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA; Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Markus Berger Oliveira
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Christopher F Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Glenn A Nardone
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Yixiang Zhang
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - B Joseph Hinnebusch
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - José M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - John F Andersen
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.
| |
Collapse
|
11
|
Dowman LJ, Agten SM, Ripoll-Rozada J, Calisto BM, Pereira PJB, Payne RJ. Synthesis and evaluation of peptidic thrombin inhibitors bearing acid-stable sulfotyrosine analogues. Chem Commun (Camb) 2021; 57:10923-10926. [PMID: 34596182 DOI: 10.1039/d1cc04742f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tyrosine sulfation is an important post-translational modification of peptides and proteins which underpins and modulates many protein-protein interactions. In order to overcome the inherent instability of the native modification, we report the synthesis of two sulfonate analogues and their incorporation into two thrombin-inhibiting sulfopeptides. The effective mimicry of these sulfonate analogues for native sulfotyrosine was validated in the context of their thrombin inhibitory activity and binding mode, as determined by X-ray crystallography.
Collapse
Affiliation(s)
- Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydne, NSW 2006, Australia
| | - Stijn M Agten
- School of Chemistry, The University of Sydney, Sydney, NSW 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
| | | | - 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
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydne, NSW 2006, Australia
| |
Collapse
|
12
|
Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
Collapse
|
13
|
Agten SM, Watson EE, Ripoll‐Rozada J, Dowman LJ, Wu MCL, Alwis I, Jackson SP, Pereira PJB, Payne RJ. Potent Trivalent Inhibitors of Thrombin through Hybridization of Salivary Sulfopeptides from Hematophagous Arthropods. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stijn M. Agten
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM) Maastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
| | - Emma E. Watson
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
| | - Jorge Ripoll‐Rozada
- IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde Universidade do Porto 4200-135 Porto Portugal
| | - Luke J. Dowman
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
| | - Mike C. L. Wu
- Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia
- Heart Research Institute Sydney NSW 2042 Australia
| | - Imala Alwis
- Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia
- Heart Research Institute Sydney NSW 2042 Australia
| | - Shaun P. Jackson
- Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia
- Heart Research Institute Sydney NSW 2042 Australia
| | - Pedro José Barbosa Pereira
- IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde Universidade do Porto 4200-135 Porto Portugal
| | - Richard J. Payne
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
| |
Collapse
|
14
|
Agten SM, Watson EE, Ripoll-Rozada J, Dowman LJ, Wu MCL, Alwis I, Jackson SP, Pereira PJB, Payne RJ. Potent Trivalent Inhibitors of Thrombin through Hybridization of Salivary Sulfopeptides from Hematophagous Arthropods. Angew Chem Int Ed Engl 2021; 60:5348-5356. [PMID: 33345438 DOI: 10.1002/anie.202015127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/14/2020] [Indexed: 12/20/2022]
Abstract
Blood feeding arthropods, such as leeches, ticks, flies and mosquitoes, provide a privileged source of peptidic anticoagulant molecules. These primarily operate through inhibition of the central coagulation protease thrombin by binding to the active site and either exosite I or exosite II. Herein, we describe the rational design of a novel class of trivalent thrombin inhibitors that simultaneously block both exosites as well as the active site. These engineered hybrids were synthesized using tandem diselenide-selenoester ligation (DSL) and native chemical ligation (NCL) reactions in one-pot. The most potent trivalent inhibitors possessed femtomolar inhibition constants against α-thrombin and were selective over related coagulation proteases. A lead hybrid inhibitor possessed potent anticoagulant activity, blockade of both thrombin generation and platelet aggregation in vitro and efficacy in a murine thrombosis model at 1 mg kg-1 . The rational engineering approach described here lays the foundation for the development of potent and selective inhibitors for a range of other enzymatic targets that possess multiple sites for the disruption of protein-protein interactions, in addition to an active site.
Collapse
Affiliation(s)
- Stijn M Agten
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Emma E Watson
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Jorge Ripoll-Rozada
- IBMC-Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Luke J Dowman
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Mike C L Wu
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Heart Research Institute, Sydney, NSW, 2042, Australia
| | - Imala Alwis
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Heart Research Institute, Sydney, NSW, 2042, Australia
| | - Shaun P Jackson
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Heart Research Institute, Sydney, NSW, 2042, Australia
| | - Pedro José Barbosa Pereira
- IBMC-Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Richard J Payne
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
| |
Collapse
|