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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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2
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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: 6] [Impact Index Per Article: 3.0] [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.
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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
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Calisto BM, Ripoll-Rozada J, Dowman LJ, Franck C, Agten SM, Parker BL, Veloso RC, Vale N, Gomes P, de Sanctis D, Payne RJ, Pereira PJB. Sulfotyrosine-Mediated Recognition of Human Thrombin by a Tsetse Fly Anticoagulant Mimics Physiological Substrates. Cell Chem Biol 2020; 28:26-33.e8. [PMID: 33096052 DOI: 10.1016/j.chembiol.2020.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/22/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022]
Abstract
Despite possessing only 32 residues, the tsetse thrombin inhibitor (TTI) is among the most potent anticoagulants described, with sub-picomolar inhibitory activity against thrombin. Unexpectedly, TTI isolated from the fly is 2000-fold more active and 180 Da heavier than synthetic and recombinant variants. We predicted the presence of a tyrosine O-sulfate post-translational modification of TTI, prompting us to investigate the effect of the modification on anticoagulant activity. A combination of chemical synthesis and functional assays was used to reveal that sulfation significantly improved the inhibitory activity of TTI against thrombin. Using X-ray crystallography, we show that the N-terminal sulfated segment of TTI binds the basic exosite II of thrombin, establishing interactions similar to those of physiologic substrates, while the C-terminal segment abolishes the catalytic activity of thrombin. This non-canonical mode of inhibition, coupled with its potency and small size, makes TTI an attractive scaffold for the design of novel antithrombotics.
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Affiliation(s)
- Bárbara M Calisto
- ESRF - The European Synchrotron, Structural Biology Group, 38000 Grenoble, France; ALBA Synchrotron, 08290 Cerdanyola del Vallès, Spain
| | - 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
| | - Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Stijn M Agten
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- Department of Physiology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Rita Carvalho Veloso
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Nuno Vale
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal; Laboratory of Pharmacology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Daniele de Sanctis
- ESRF - The European Synchrotron, Structural Biology Group, 38000 Grenoble, France
| | - 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 Sydney, Sydney, NSW 2006, 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.
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Pinto MF, Figueiredo F, Silva A, Pombinho AR, Pereira PJB, Macedo-Ribeiro S, Rocha F, Martins PM. Major Improvements in Robustness and Efficiency during the Screening of Novel Enzyme Effectors by the 3-Point Kinetics Assay. SLAS DISCOVERY 2020; 26:373-382. [PMID: 32981414 DOI: 10.1177/2472555220958386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The throughput level currently reached by automatic liquid handling and assay monitoring techniques is expected to facilitate the discovery of new modulators of enzyme activity. Judicious and dependable ways to interpret vast amounts of information are, however, required to effectively answer this challenge. Here, the 3-point method of kinetic analysis is proposed as a means to significantly increase the hit success rates and decrease the number of falsely identified compounds (false positives). In this post-Michaelis-Menten approach, each screened reaction is probed in three different occasions, none of which necessarily coincide with the initial period of constant velocity. Enzymology principles rather than subjective criteria are applied to identify unwanted outliers such as assay artifacts, and then to accurately distinguish true enzyme modulation effects from false positives. The exclusion and selection criteria are defined based on the 3-point reaction coordinates, whose relative positions along the time-courses may change from well to well or from plate to plate, if necessary. The robustness and efficiency of the new method is illustrated during a small drug repurposing screening of potential modulators of the deubiquinating activity of ataxin-3, a protein implicated in Machado-Joseph disease. Apparently, intractable Z factors are drastically enhanced after (1) eliminating spurious results, (2) improving the normalization method, and (3) increasing the assay resilience to systematic and random variability. Numerical simulations further demonstrate that the 3-point analysis is highly sensitive to specific, catalytic, and slow-onset modulation effects that are particularly difficult to detect by typical endpoint assays.
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Affiliation(s)
- Maria Filipa Pinto
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal.,Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia (LEPABE), Faculdade de Engenharia da Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory (INL), Braga, Portugal
| | - Alexandra Silva
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - António R Pombinho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Fernando Rocha
- Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia (LEPABE), Faculdade de Engenharia da Universidade do Porto, Porto, Portugal
| | - Pedro M Martins
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
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Pinto MF, Baici A, Pereira PJB, Macedo-Ribeiro S, Pastore A, Rocha F, Martins PM. interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis. J Mol Biol 2020; 433:166613. [PMID: 32768452 DOI: 10.1016/j.jmb.2020.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 02/01/2023]
Abstract
Enzymatic assays are widely employed to characterize important allosteric and enzyme modulation effects. The high sensitivity of these assays can represent a serious problem if the occurrence of experimental errors surreptitiously affects the reliability of enzyme kinetics results. We have addressed this problem and found that hidden assay interferences can be unveiled by the graphical representation of progress curves in modified reaction coordinates. To render this analysis accessible to users across all levels of expertise, we have developed a webserver, interferENZY, that allows (i) an unprecedented tight quality control of experimental data, (ii) the automated identification of small and major assay interferences, and (iii) the estimation of bias-free kinetic parameters. By eliminating the subjectivity factor in kinetic data reporting, interferENZY will contribute to solving the "reproducibility crisis" that currently challenges experimental molecular biology. The interferENZY webserver is freely available (no login required) at https://interferenzy.i3s.up.pt.
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Affiliation(s)
- Maria Filipa Pinto
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; LEPABE-Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Antonio Baici
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Pedro José Barbosa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Annalisa Pastore
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Rd, Brixton, London SE5 9RT, England, UK
| | - Fernando Rocha
- LEPABE-Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Pedro M Martins
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
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Halling PJ. Estimation of initial rate from discontinuous progress data. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1746771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Peter J. Halling
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
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