1
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Hommel K, Kauth AMA, Kirupakaran A, Theisen S, Hayduk M, Niemeyer FC, Beuck C, Zadmard R, Bayer P, Jan Ravoo B, Voskuhl J, Schrader T, Knauer SK. Functional Linkers Support Targeting of Multivalent Tweezers to Taspase1. Chemistry 2024:e202401542. [PMID: 38958349 DOI: 10.1002/chem.202401542] [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: 04/20/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Taspase 1 is a unique protease not only pivotal for embryonic development but also implicated in leukemias and solid tumors. As such, this enzyme is a promising while still challenging therapeutic target, and with its protein structure featuring a flexible loop preceding the active site a versatile model system for drug development. Supramolecular ligands provide a promising complementary approach to traditional small-molecule inhibitors. Recently, the multivalent arrangement of molecular tweezers allowed the successful targeting of Taspase 1's surface loop. With this study we now want to take the next logic step und utilize functional linker systems that not only allow the implementation of novel properties but also engage in protein surface binding. Consequently, we chose two different linker types differing from the original divalent assembly: a backbone with aggregation-induced emission (AIE) properties to enable monitoring of binding and a calix[4]arene scaffold initially pre-positioning the supramolecular binding units. With a series of four AIE-equipped ligands with stepwise increased valency we demonstrated that the functionalized AIE linkers approach ligand binding affinities in the nanomolar range and allow efficient proteolytic inhibition of Taspase 1. Moreover, implementation of the calix[4]arene backbone further enhanced the ligands' inhibitory potential, pointing to a specific linker contribution.
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Affiliation(s)
- Katrin Hommel
- Molecular Biology II, Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Alisa-Maite A Kauth
- Organic Chemistry Institute and Center for Soft Nanoscience, University of Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Sebastian Theisen
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Matthias Hayduk
- Faculty of Chemistry (Organic Chemistry II), Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Reza Zadmard
- Department of Organic Chemistry, Chemistry and Chemical Engineering Research Center of Iran (CCERCI), P. O. Box 14335-186, Tehran, Iran
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Bart Jan Ravoo
- Organic Chemistry Institute and Center for Soft Nanoscience, University of Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Jens Voskuhl
- Faculty of Chemistry (Organic Chemistry II), Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
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2
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Flood R, Cerofolini L, Fragai M, Crowley PB. Multivalent Calixarene Complexation of a Designed Pentameric Lectin. Biomacromolecules 2024; 25:1303-1309. [PMID: 38227741 PMCID: PMC10865345 DOI: 10.1021/acs.biomac.3c01280] [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: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
We describe complex formation between a designed pentameric β-propeller and the anionic macrocycle sulfonato-calix[8]arene (sclx8), as characterized by X-ray crystallography and NMR spectroscopy. Two crystal structures and 15N HSQC experiments reveal a single calixarene binding site in the concave pocket of the β-propeller toroid. Despite the symmetry mismatch between the pentameric protein and the octameric macrocycle, they form a high affinity multivalent complex, with the largest protein-calixarene interface observed to date. This system provides a platform for investigating multivalency.
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Affiliation(s)
- Ronan
J. Flood
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Linda Cerofolini
- Magnetic
Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
| | - Peter B. Crowley
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
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3
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Seiler T, Lennartz A, Klein K, Hommel K, Figueroa Bietti A, Hadrovic I, Kollenda S, Sager J, Beuck C, Chlosta E, Bayer P, Juul-Madsen K, Vorup-Jensen T, Schrader T, Epple M, Knauer SK, Hartmann L. Potentiating Tweezer Affinity to a Protein Interface with Sequence-Defined Macromolecules on Nanoparticles. Biomacromolecules 2023; 24:3666-3679. [PMID: 37507377 DOI: 10.1021/acs.biomac.3c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Survivin, a well-known member of the inhibitor of apoptosis protein family, is upregulated in many cancer cells, which is associated with resistance to chemotherapy. To circumvent this, inhibitors are currently being developed to interfere with the nuclear export of survivin by targeting its protein-protein interaction (PPI) with the export receptor CRM1. Here, we combine for the first time a supramolecular tweezer motif, sequence-defined macromolecular scaffolds, and ultrasmall Au nanoparticles (us-AuNPs) to tailor a high avidity inhibitor targeting the survivin-CRM1 interaction. A series of biophysical and biochemical experiments, including surface plasmon resonance measurements and their multivalent evaluation by EVILFIT, reveal that for divalent macromolecular constructs with increasing linker distance, the longest linkers show superior affinity, slower dissociation, as well as more efficient PPI inhibition. As a drawback, these macromolecular tweezer conjugates do not enter cells, a critical feature for potential applications. The problem is solved by immobilizing the tweezer conjugates onto us-AuNPs, which enables efficient transport into HeLa cells. On the nanoparticles, the tweezer valency rises from 2 to 16 and produces a 100-fold avidity increase. The hierarchical combination of different scaffolds and controlled multivalent presentation of supramolecular binders was the key to the development of highly efficient survivin-CRM1 competitors. This concept may also be useful for other PPIs.
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Affiliation(s)
- Theresa Seiler
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstraße 1, Duesseldorf 40225, Germany
| | - Annika Lennartz
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Kai Klein
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Katrin Hommel
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Antonio Figueroa Bietti
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Inesa Hadrovic
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Sebastian Kollenda
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Jonas Sager
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Emilia Chlosta
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Kristian Juul-Madsen
- Department of Biomedicine, Aarhus University, Skou Building (1115), Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark
- Max-Delbrueck-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Vorup-Jensen
- Department of Biomedicine, Aarhus University, Skou Building (1115), Høegh-Guldbergs Gade 10, DK-8000 Aarhus C, Denmark
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 5-7, Essen 45117, Germany
| | - Shirley K Knauer
- Department for Molecular Biology II, Center of Medical Biotechnology (ZMB), University Duisburg-Essen, Universitaetsstrasse 5, Essen 45117, Germany
| | - Laura Hartmann
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstraße 1, Duesseldorf 40225, Germany
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4
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Neblik J, Kirupakaran A, Beuck C, Mieres-Perez J, Niemeyer F, Le MH, Telgheder U, Schmuck JF, Dudziak A, Bayer P, Sanchez-Garcia E, Westermann S, Schrader T. Multivalent Molecular Tweezers Disrupt the Essential NDC80 Interaction with Microtubules. J Am Chem Soc 2023. [PMID: 37392180 DOI: 10.1021/jacs.3c02186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
Binding of microtubule filaments by the conserved Ndc80 protein is required for kinetochore-microtubule attachments in cells and the successful distribution of the genetic material during cell division. The reversible inhibition of microtubule binding is an important aspect of the physiological error correction process. Small molecule inhibitors of protein-protein interactions involving Ndc80 are therefore highly desirable, both for mechanistic studies of chromosome segregation and also for their potential therapeutic value. Here, we report on a novel strategy to develop rationally designed inhibitors of the Ndc80 Calponin-homology domain using Supramolecular Chemistry. With a multiple-click approach, lysine-specific molecular tweezers were assembled to form covalently fused dimers to pentamers with a different overall size and preorganization/stiffness. We identified two dimers and a trimer as efficient Ndc80 CH-domain binders and have shown that they disrupt the interaction between Ndc80 and microtubules at low micromolar concentrations without affecting microtubule dynamics. NMR spectroscopy allowed us to identify the biologically important lysine residues 160 and 204 as preferred tweezer interaction sites. Enhanced sampling molecular dynamics simulations provided a rationale for the binding mode of multivalent tweezers and the role of pre-organization and secondary interactions in targeting multiple lysine residues across a protein surface.
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Affiliation(s)
- Jonas Neblik
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Abbna Kirupakaran
- Faculty of Chemistry, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Christine Beuck
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Joel Mieres-Perez
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
- Computational Bioengineering, Faculty of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, North Rhine-Westfalia 44227, Germany
| | - Felix Niemeyer
- Faculty of Chemistry, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - My-Hue Le
- Faculty of Chemistry, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Ursula Telgheder
- Faculty of Chemistry, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Jessica Felice Schmuck
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Alexander Dudziak
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Peter Bayer
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Elsa Sanchez-Garcia
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
- Computational Bioengineering, Faculty of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, North Rhine-Westfalia 44227, Germany
| | - Stefan Westermann
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, North Rhine-Westfalia 45141, Germany
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5
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Höing A, Struth R, Beuck C, Rafieiolhosseini N, Hoffmann D, Stauber RH, Bayer P, Niemeyer J, Knauer SK. Dual activity inhibition of threonine aspartase 1 by a single bisphosphate ligand. RSC Adv 2022; 12:34176-34184. [PMID: 36545626 PMCID: PMC9709806 DOI: 10.1039/d2ra06019a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Therapy resistance remains a challenge for the clinics. Here, dual-active chemicals that simultaneously inhibit independent functions in disease-relevant proteins are desired though highly challenging. As a model, we here addressed the unique protease threonine aspartase 1, involved in various cancers. We hypothesized that targeting basic residues in its bipartite nuclear localization signal (NLS) by precise bisphosphate ligands inhibits additional steps required for protease activity. We report the bisphosphate anionic bivalent inhibitor 11d, selectively binding to the basic NLS cluster (220KKRR223) with high affinity (K D = 300 nM), thereby disrupting its interaction and function with Importin α (IC50 = 6 μM). Cell-free assays revealed that 11d additionally affected the protease's catalytic substrate trans-cleavage activity. Importantly, functional assays comprehensively demonstrated that 11d inhibited threonine aspartase 1 also in living tumor cells. We demonstrate for the first time that intracellular interference with independent key functions in a disease-relevant protein by an inhibitor binding to a single site is possible.
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Affiliation(s)
- Alexander Höing
- Molecular Biology II, Center of Medical Biotechnology (ZMB)/Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5 45141 Essen Germany
| | - Robin Struth
- Organic Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7 45141 Essen Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5 45141 Essen Germany
| | - Neda Rafieiolhosseini
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5 45141 Essen Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5 45141 Essen Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology/ENT, University Medical Center Mainz (UMM) Langenbeckstrasse 1 55101 Mainz Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5 45141 Essen Germany
| | - Jochen Niemeyer
- Organic Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7 45141 Essen Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB)/Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5 45141 Essen Germany
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