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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] [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 545141 EssenGermany
| | - Robin Struth
- Organic Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 745141 EssenGermany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 545141 EssenGermany
| | - Neda Rafieiolhosseini
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 545141 EssenGermany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 545141 EssenGermany
| | - Roland H. Stauber
- Molecular and Cellular Oncology/ENT, University Medical Center Mainz (UMM)Langenbeckstrasse 155101 MainzGermany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 545141 EssenGermany
| | - Jochen Niemeyer
- Organic Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 745141 EssenGermany
| | - Shirley K. Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB)/Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 545141 EssenGermany
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SeqCP: A sequence-based algorithm for searching circularly permuted proteins. Comput Struct Biotechnol J 2022; 21:185-201. [PMID: 36582435 PMCID: PMC9763678 DOI: 10.1016/j.csbj.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence. Circularly permutated proteins usually exhibit conserved three-dimensional structures and functions. By comparing the structures of circular permutants (CPMs), protein research and bioengineering applications can be approached in ways that are difficult to achieve by traditional mutagenesis. Most current CP detection algorithms depend on structural information. Because there is a vast number of proteins with unknown structures, many CP pairs may remain unidentified. An efficient sequence-based CP detector will help identify more CP pairs and advance many protein studies. For instance, some hypothetical proteins may have CPMs with known functions and structures that are informative for functional annotation, but existing structure-based CP search methods cannot be applied when those hypothetical proteins lack structural information. Despite the considerable potential for applications, sequence-based CP search methods have not been well developed. We present a sequence-based method, SeqCP, which analyzes normal and duplicated sequence alignments to identify CPMs and determine candidate CP sites for proteins. SeqCP was trained by data obtained from the Circular Permutation Database and tested with nonredundant datasets from the Protein Data Bank. It shows high reliability in CP identification and achieves an AUC of 0.9. SeqCP has been implemented into a web server available at: http://pcnas.life.nthu.edu.tw/SeqCP/.
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Key Words
- AUC, area under the ROC curve
- CE, combinatorial extension
- CE-CP, CE with Circular Permutations
- CP, circular permutation
- CPDB, Circular Permutation Database
- CPMs, circular permutants
- CPSARST, Circular Permutation Search Aided by Ramachandran Sequential Transformation
- Circular permutants
- Circular permutation
- MCC, Matthews correlation coefficient
- Protein sequence analysis
- Protein structure modeling
- RMSD, root-mean-square distance
- ROC, receiver operating characteristic
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Höing A, Kirupakaran A, Beuck C, Pörschke M, Niemeyer FC, Seiler T, Hartmann L, Bayer P, Schrader T, Knauer SK. Recognition of a Flexible Protein Loop in Taspase 1 by Multivalent Supramolecular Tweezers. Biomacromolecules 2022; 23:4504-4518. [PMID: 36200481 DOI: 10.1021/acs.biomac.2c00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many natural proteins contain flexible loops utilizing well-defined complementary surface regions of their interacting partners and usually undergo major structural rearrangements to allow perfect binding. The molecular recognition of such flexible structures is still highly challenging due to the inherent conformational dynamics. Notably, protein-protein interactions are on the other hand characterized by a multivalent display of complementary binding partners to enhance molecular affinity and specificity. Imitating this natural concept, we here report the rational design of advanced multivalent supramolecular tweezers that allow addressing two lysine and arginine clusters on a flexible protein surface loop. The protease Taspase 1, which is involved in cancer development, carries a basic bipartite nuclear localization signal (NLS) and thus interacts with Importin α, a prerequisite for proteolytic activation. Newly established synthesis routes enabled us to covalently fuse several tweezer molecules into multivalent NLS ligands. The resulting bi- up to pentavalent constructs were then systematically compared in comprehensive biochemical assays. In this series, the stepwise increase in valency was robustly reflected by the ligands' gradually enhanced potency to disrupt the interaction of Taspase 1 with Importin α, correlated with both higher binding affinity and inhibition of proteolytic activity.
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Affiliation(s)
- Alexander Höing
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, 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
| | - Marius Pörschke
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Theresa Seiler
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
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Closantel is an allosteric inhibitor of human Taspase1. iScience 2021; 24:103524. [PMID: 34934933 DOI: 10.1016/j.isci.2021.103524] [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: 08/02/2021] [Revised: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 11/23/2022] Open
Abstract
Dimerization of Taspase1 activates an intrinsic serine protease function that leads to the catalytic Thr234 residue, which allows to catalyze the consensus sequence Q-3X-2D-1⋅G1X2D3D4, present in Trithorax family members and TFIIA. Noteworthy, Taspase1 performs only a single hydrolytic step on substrate proteins, which makes it impossible to screen for inhibitors in a classical screening approach. Here, we report the development of an HTRF reporter assay that allowed the identification of an inhibitor, Closantel sodium, that inhibits Taspase1 in a noncovalent fashion (IC50 = 1.6 μM). The novel inhibitor interferes with the dimerization step and/or the intrinsic serine protease function of the proenzyme. Of interest, Taspase1 is required to activate the oncogenic functions of the leukemogenic AF4-MLL fusion protein and was shown in several studies to be overexpressed in many solid tumors. Therefore, the inhibitor may be useful for further validation of Taspase1 as a target for cancer therapy.
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