1
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Sele C, Krupinska E, Andersson Rasmussen A, Ekström S, Hultgren L, Lou J, Kozielski F, Fisher SZ, Knecht W. New insights into complex formation by SARS-CoV-2 nsp10 and nsp14. Nucleosides Nucleotides Nucleic Acids 2024:1-15. [PMID: 38422227 DOI: 10.1080/15257770.2024.2321600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
SARS-CoV-2 non-structural protein 10 (nsp10) is essential for the stimulation of enzymatic activities of nsp14 and nsp16, acting as both an activator and scaffolding protein. Nsp14 is a bifunctional enzyme with the N-terminus containing a 3'-5' exoribonuclease (ExoN) domain that allows the excision of nucleotide mismatches at the virus RNA 3'-end, and a C-terminal N7-methyltransferase (N7-MTase) domain. Nsp10 is required for stimulating both ExoN proofreading and the nsp16 2'-O-methyltransferase activities. This makes nsp10 a central player in both viral resistance to nucleoside-based drugs and the RNA cap methylation machinery that helps the virus evade innate immunity. We characterised the interactions between full-length nsp10 (139 residues), N- and C-termini truncated nsp10 (residues 10-133), and nsp10 with a C-terminal truncation (residues 1-133) with nsp14 using microscale thermophoresis, multi-detection SEC, and hydrogen-deuterium (H/D) exchange mass spectrometry. We describe the functional role of the C-terminal region of nsp10 for binding to nsp14 and show that full N- and C-termini of nsp10 are important for optimal binding. In addition, our H/D exchange experiments suggest an intermediary interaction of nsp10 with the N7-MTase domain of nsp14. In summary, our results suggest intermediary steps in the process of association or dissociation of the nsp10-nsp14 complex, involving contacts between the two proteins in regions not identifiable by X-ray crystallography alone.
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Affiliation(s)
- Céleste Sele
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Lund, Sweden
| | - Ewa Krupinska
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Lund, Sweden
| | - Anna Andersson Rasmussen
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Lund, Sweden
| | - Simon Ekström
- Swedish National Infrastructure for Biological Mass Spectrometry and SciLifeLab, Integrated Structural Biology platform, Structural Proteomics Unit Sweden, Lund University, Lund, Sweden
| | - Lucas Hultgren
- Swedish National Infrastructure for Biological Mass Spectrometry and SciLifeLab, Integrated Structural Biology platform, Structural Proteomics Unit Sweden, Lund University, Lund, Sweden
| | - Jiaqi Lou
- School of Pharmacy, University College London, London, UK
| | | | - S Zoë Fisher
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Lund, Sweden
- European Spallation Source ERIC, Lund, Sweden
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Lund, Sweden
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2
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Wang H, Rizvi SRA, Dong D, Lou J, Wang Q, Sopipong W, Su Y, Najar F, Agarwal PK, Kozielski F, Haider S. Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16. eLife 2023; 12:RP87884. [PMID: 38127066 PMCID: PMC10735223 DOI: 10.7554/elife.87884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5' end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2'-O-methyltransferase and NSP14 through its N7 methyltransferase activity, which are essential for the replication of the viral genome as well as evading the host's innate immunity. NSP10 acts as a crucial cofactor and stimulator of NSP14 and NSP16. To further understand the role of NSP10, we carried out a comprehensive analysis of >13 million globally collected whole-genome sequences (WGS) of SARS-CoV-2 obtained from the Global Initiative Sharing All Influenza Data (GISAID) and compared it with the reference genome Wuhan/WIV04/2019 to identify all currently known variants in NSP10. T12I, T102I, and A104V in NSP10 have been identified as the three most frequent variants and characterized using X-ray crystallography, biophysical assays, and enhanced sampling simulations. In contrast to other proteins such as spike and NSP6, NSP10 is significantly less prone to mutation due to its crucial role in replication. The functional effects of the variants were examined for their impact on the binding affinity and stability of both NSP14-NSP10 and NSP16-NSP10 complexes. These results highlight the limited changes induced by variant evolution in NSP10 and reflect on the critical roles NSP10 plays during the SARS-CoV-2 life cycle. These results also indicate that there is limited capacity for the virus to overcome inhibitors targeting NSP10 via the generation of variants in inhibitor binding pockets.
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Affiliation(s)
- Huan Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Syed RA Rizvi
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Danni Dong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Jiaqi Lou
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Qian Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Watanyoo Sopipong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Yufeng Su
- College of Engineering, Design and Physical Sciences, Brunel University LondonUxbridgeUnited Kingdom
| | - Fares Najar
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Pratul K Agarwal
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
- UCL Centre for Advanced Research Computing, University College LondonLondonUnited Kingdom
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3
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Tang J, Zhang C, Castillo NC, Lalaurie CJ, Gao X, Dalby PA, Kozielski F. Crystal structures and molecular dynamics simulations of a humanised antibody fragment at acidic to basic pH. Sci Rep 2023; 13:16281. [PMID: 37770469 PMCID: PMC10539359 DOI: 10.1038/s41598-023-42698-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Antibody-fragment (Fab) therapy development has the potential to be accelerated by computational modelling and simulations that predict their target binding, stability, formulation, manufacturability, and the impact of further protein engineering. Such approaches are currently predicated on starting with good crystal structures that closely represent those found under the solution conditions to be simulated. A33 Fab, is an undeveloped immunotherapeutic antibody candidate that was targeted to the human A33 antigen homogeneously expressed in 95% cases of primary and metastatic colorectal cancers. It is now used as a very well characterised testing ground for developing analytics, formulation and protein engineering strategies, and to gain a deeper understanding of mechanisms of destabilisation, representative of the wider therapeutic Fab platform. In this article, we report the structure of A33 Fab in two different crystal forms obtained at acidic and basic pH. The structures overlapped with RMSD of 1.33 Å overall, yet only 0.5 Å and 0.76 Å for the variable- and constant regions alone. While most of the differences were within experimental error, the switch linker between the variable and the constant regions showed some small differences between the two pHs. The two structures then enabled a direct evaluation of the impact of initial crystal structure selection on the outcomes of molecular dynamics simulations under different conditions, and their subsequent use for determining best fit solution structures using previously obtained small-angle x-ray scattering (SAXS) data. The differences in the two structures did not have a major impact on MD simulations regardless of the pH, other than a slight persistence of structure affecting the solvent accessibility of one of the predicted APR regions of A33 Fab. Interestingly, despite being obtained at pH 4 and pH 9, the two crystal structures were more similar to the SAXS solution structures obtained at pH 7, than to those at pH 4 or pH 9. Furthermore, the P65 crystal structure from pH 4 was also a better representation of the solution structures at any other pH, than was the P1 structure obtained at pH 9. Thus, while obtained at different pH, the two crystal structures may represent highly (P65) and lesser (P1) populated species that both exist at pH 7 in solution. These results now lay the foundation for confident MD simulations of A33 Fab that rationalise or predict behaviours in a range of conditions.
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Affiliation(s)
- Jiazhi Tang
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Cheng Zhang
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Nuria Codina Castillo
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Christophe J Lalaurie
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Xin Gao
- Division of Biosciences, Department of Structural and Molecular Biology, UCL, London, WC1E 6BT, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
| | - Frank Kozielski
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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4
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Knecht W, Fisher SZ, Lou J, Sele C, Ma S, Rasmussen AA, Pinotsis N, Kozielski F. Oligomeric State of β-Coronavirus Non-Structural Protein 10 Stimulators Studied by Small Angle X-ray Scattering. Int J Mol Sci 2023; 24:13649. [PMID: 37686452 PMCID: PMC10563069 DOI: 10.3390/ijms241713649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The β-coronavirus family, encompassing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Severe Acute Respiratory Syndrome Coronavirus (SARS), and Middle East Respiratory Syndrome Coronavirus (MERS), has triggered pandemics within the last two decades. With the possibility of future pandemics, studying the coronavirus family members is necessary to improve knowledge and treatment. These viruses possess 16 non-structural proteins, many of which play crucial roles in viral replication and in other vital functions. One such vital protein is non-structural protein 10 (nsp10), acting as a pivotal stimulator of nsp14 and nsp16, thereby influencing RNA proofreading and viral RNA cap formation. Studying nsp10 of pathogenic coronaviruses is central to unraveling its multifunctional roles. Our study involves the biochemical and biophysical characterisation of full-length nsp10 from MERS, SARS and SARS-CoV-2. To elucidate their oligomeric state, we employed a combination of Multi-detection Size exclusion chromatography (Multi-detection SEC) with multi-angle static light scattering (MALS) and small angle X-ray scattering (SAXS) techniques. Our findings reveal that full-length nsp10s primarily exist as monomers in solution, while truncated versions tend to oligomerise. SAXS experiments reveal a globular shape for nsp10, a trait conserved in all three coronaviruses, although MERS nsp10, diverges most from SARS and SARS-CoV-2 nsp10s. In summary, unbound nsp10 proteins from SARS, MERS, and SARS-CoV-2 exhibit a globular and predominantly monomeric state in solution.
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Affiliation(s)
- Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
| | - S. Zoë Fisher
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
- European Spallation Source ERIC, P.O. Box 176, 22100 Lund, Sweden
| | - Jiaqi Lou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (J.L.); (S.M.)
| | - Céleste Sele
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
| | - Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (J.L.); (S.M.)
| | - Anna Andersson Rasmussen
- Department of Biology & Lund Protein Production Platform & Protein Production Sweden, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (W.K.); (S.Z.F.); (C.S.); (A.A.R.)
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (J.L.); (S.M.)
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5
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Ma S, Mykhaylyk V, Bowler MW, Pinotsis N, Kozielski F. High-Confidence Placement of Fragments into Electron Density Using Anomalous Diffraction-A Case Study Using Hits Targeting SARS-CoV-2 Non-Structural Protein 1. Int J Mol Sci 2023; 24:11197. [PMID: 37446375 DOI: 10.3390/ijms241311197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
The identification of multiple simultaneous orientations of small molecule inhibitors binding to a protein target is a common challenge. It has recently been reported that the conformational heterogeneity of ligands is widely underreported in the Protein Data Bank, which is likely to impede optimal exploitation to improve affinity of these ligands. Significantly less is even known about multiple binding orientations for fragments (<300 Da), although this information would be essential for subsequent fragment optimisation using growing, linking or merging and rational structure-based design. Here, we use recently reported fragment hits for the SARS-CoV-2 non-structural protein 1 (nsp1) N-terminal domain to propose a general procedure for unambiguously identifying binding orientations of 2-dimensional fragments containing either sulphur or chloro substituents within the wavelength range of most tunable beamlines. By measuring datasets at two energies, using a tunable beamline operating in vacuum and optimised for data collection at very low X-ray energies, we show that the anomalous signal can be used to identify multiple orientations in small fragments containing sulphur and/or chloro substituents or to verify recently reported conformations. Although in this specific case we identified the positions of sulphur and chlorine in fragments bound to their protein target, we are confident that this work can be further expanded to additional atoms or ions which often occur in fragments. Finally, our improvements in the understanding of binding orientations will also serve to improve the rational optimisation of SARS-CoV-2 nsp1 fragment hits.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | | | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
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6
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Wagstaff JM, Planelles-Herrero VJ, Sharov G, Alnami A, Kozielski F, Derivery E, Löwe J. Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics. Sci Adv 2023; 9:eadf3021. [PMID: 36989372 PMCID: PMC10058229 DOI: 10.1126/sciadv.adf3021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart.
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Affiliation(s)
- James Mark Wagstaff
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Grigory Sharov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Aisha Alnami
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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7
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Borsatto A, Akkad O, Galdadas I, Ma S, Damfo S, Haider S, Kozielski F, Estarellas C, Gervasio FL. Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography. eLife 2022; 11:81167. [DOI: 10.7554/elife.81167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/06/2022] [Indexed: 11/23/2022] Open
Abstract
Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α- and β-coronaviruses. Nsp1 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S host ribosomal subunits and promoting host mRNA degradation. This mechanism leads to the downregulation of the translation-mediated innate immune response in host cells, ultimately mediating the observed immune evasion capabilities of SARS-CoV-2. Here, by combining extensive molecular dynamics simulations, fragment screening and crystallography, we reveal druggable pockets in Nsp1. Structural and computational solvent mapping analyses indicate the partial crypticity of these newly discovered and druggable binding sites. The results of fragment-based screening via X-ray crystallography confirm the druggability of the major pocket of Nsp1. Finally, we show how the targeting of this pocket could disrupt the Nsp1-mRNA complex and open a novel avenue to design new inhibitors for other Nsp1s present in homologous β-coronaviruses.
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Affiliation(s)
- Alberto Borsatto
- School of Pharmaceutical Sciences, University of Geneva
- ISPSO, University of Geneva
| | - Obaeda Akkad
- School of Pharmaceutical Sciences, University of Geneva
- ISPSO, University of Geneva
| | - Ioannis Galdadas
- School of Pharmaceutical Sciences, University of Geneva
- ISPSO, University of Geneva
| | - Shumeng Ma
- School of Pharmacy, University College London
| | | | - Shozeb Haider
- School of Pharmacy, University College London
- UCL Centre for Advanced Research Computing, University College London
| | | | - Carolina Estarellas
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Theoretical and Computational Chemistry, University of Barcelona
| | - Francesco Luigi Gervasio
- School of Pharmaceutical Sciences, University of Geneva
- ISPSO, University of Geneva
- Chemistry Department, University College London
- Institute of Structural and Molecular Biology, University College London
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8
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Ma S, Damfo S, Lou J, Pinotsis N, Bowler MW, Haider S, Kozielski F. Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening. Int J Mol Sci 2022; 23:ijms232012448. [PMID: 36293303 PMCID: PMC9604401 DOI: 10.3390/ijms232012448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
The regular reappearance of coronavirus (CoV) outbreaks over the past 20 years has caused significant health consequences and financial burdens worldwide. The most recent and still ongoing novel CoV pandemic, caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has brought a range of devastating consequences. Due to the exceptionally fast development of vaccines, the mortality rate of the virus has been curbed to a significant extent. However, the limitations of vaccination efficiency and applicability, coupled with the still high infection rate, emphasise the urgent need for discovering safe and effective antivirals against SARS-CoV-2 by suppressing its replication or attenuating its virulence. Non-structural protein 1 (nsp1), a unique viral and conserved leader protein, is a crucial virulence factor for causing host mRNA degradation, suppressing interferon (IFN) expression and host antiviral signalling pathways. In view of the essential role of nsp1 in the CoV life cycle, it is regarded as an exploitable target for antiviral drug discovery. Here, we report a variety of fragment hits against the N-terminal domain of SARS-CoV-2 nsp1 identified by fragment-based screening via X-ray crystallography. We also determined the structure of nsp1 at atomic resolution (0.99 Å). Binding affinities of hits against nsp1 and potential stabilisation were determined by orthogonal biophysical assays such as microscale thermophoresis and thermal shift assays. We identified two ligand-binding sites on nsp1, one deep and one shallow pocket, which are not conserved between the three medically relevant SARS, SARS-CoV-2 and MERS coronaviruses. Our study provides an excellent starting point for the development of more potent nsp1-targeting inhibitors and functional studies on SARS-CoV-2 nsp1.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shymaa Damfo
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiaqi Lou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | | | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- Correspondence:
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9
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Georgakopoulos N, Talapatra S, Dikovskaya D, Dayalan Naidu S, Higgins M, Gatliff J, Ayhan A, Nikoloudaki R, Schaap M, Valko K, Javid F, Dinkova-Kostova AT, Kozielski F, Wells G. Phenyl Bis-Sulfonamide Keap1-Nrf2 Protein-Protein Interaction Inhibitors with an Alternative Binding Mode. J Med Chem 2022; 65:7380-7398. [PMID: 35549469 PMCID: PMC9150106 DOI: 10.1021/acs.jmedchem.2c00457] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 11/29/2022]
Abstract
Inhibitors of Kelch-like ECH-associated protein 1 (Keap1) increase the activity of the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) by stalling its ubiquitination and degradation. This enhances the expression of genes encoding proteins involved in drug detoxification, redox homeostasis, and mitochondrial function. Nrf2 activation offers a potential therapeutic approach for conditions including Alzheimer's and Parkinson's diseases, vascular inflammation, and chronic obstructive airway disease. Non-electrophilic Keap1-Nrf2 protein-protein interaction (PPI) inhibitors may have improved toxicity profiles and different pharmacological properties to cysteine-reactive electrophilic inhibitors. Here, we describe and characterize a series of phenyl bis-sulfonamide PPI inhibitors that bind to Keap1 at submicromolar concentrations. Structural studies reveal that the compounds bind to Keap1 in a distinct "peptidomimetic" conformation that resembles the Keap1-Nrf2 ETGE peptide complex. This is different to other small molecule Keap1-Nrf2 PPI inhibitors, including bicyclic aryl bis-sulfonamides, offering a starting point for new design approaches to Keap1 inhibitors.
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Affiliation(s)
- Nikolaos Georgakopoulos
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
- Stevenage
Bioscience Catalyst, Keregen Therapeutics
Ltd., Gunnels Wood Rd, Stevenage SG1 2FX, U.K.
| | - Sandeep Talapatra
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
| | - Dina Dikovskaya
- Jacqui
Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, U.K.
| | - Sharadha Dayalan Naidu
- Jacqui
Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, U.K.
| | - Maureen Higgins
- Jacqui
Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, U.K.
| | - Jemma Gatliff
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
- Stevenage
Bioscience Catalyst, Keregen Therapeutics
Ltd., Gunnels Wood Rd, Stevenage SG1 2FX, U.K.
| | - Aysel Ayhan
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
| | - Roxani Nikoloudaki
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
- Stevenage
Bioscience Catalyst, Keregen Therapeutics
Ltd., Gunnels Wood Rd, Stevenage SG1 2FX, U.K.
| | - Marjolein Schaap
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
| | - Klara Valko
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
- Bio-Mimetic
Chromatography Consultancy, 17 Cabot Close, Stevenage SG2 0ES, U.K.
| | - Farideh Javid
- Department
of Pharmacy, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, U.K.
| | - Albena T. Dinkova-Kostova
- Jacqui
Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, U.K.
- Department
of Pharmacology and Molecular Sciences and Department of Medicine,
School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Frank Kozielski
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
| | - Geoffrey Wells
- UCL
School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, U.K.
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10
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Kozielski F, Sele C, Talibov VO, Lou J, Dong D, Wang Q, Shi X, Nyblom M, Rogstam A, Krojer T, Fisher Z, Knecht W. Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16. RSC Chem Biol 2022; 3:44-55. [PMID: 35128408 PMCID: PMC8729259 DOI: 10.1039/d1cb00135c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
Since the emergence of SARS-CoV-2 in 2019, Covid-19 has developed into a serious threat to our health, social and economic systems. Although vaccines have been developed in a tour-de-force and are now increasingly available, repurposing of existing drugs has been less successful. There is a clear need to develop new drugs against SARS-CoV-2 that can also be used against future coronavirus infections. Non-structural protein 10 (nsp10) is a conserved stimulator of two enzymes crucial for viral replication, nsp14 and nsp16, exhibiting exoribonuclease and methyltransferase activities. Interfering with RNA proofreading or RNA cap formation represents intervention strategies to inhibit replication. We applied fragment-based screening using nano differential scanning fluorometry and X-ray crystallography to identify ligands targeting SARS-CoV-2 nsp10. We identified four fragments located in two distinct sites: one can be modelled to where it would be located in the nsp14-nsp10 complex interface and the other in the nsp16-nsp10 complex interface. Microscale thermophoresis (MST) experiments were used to quantify fragment affinities for nsp10. Additionally, we showed by MST that the interaction by nsp14 and 10 is weak and thereby that complex formation could be disrupted by small molecules. The fragments will serve as starting points for the development of more potent analogues using fragment growing techniques and structure-based drug design.
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Affiliation(s)
- Frank Kozielski
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Céleste Sele
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | | | - Jiaqi Lou
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Danni Dong
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Qian Wang
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Xinyue Shi
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Maria Nyblom
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | - Annika Rogstam
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | - Tobias Krojer
- BioMAX beamline, MAX IV Laboratory Fotongatan 2 22484 Lund Sweden
| | - Zoë Fisher
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
- European Spallation Source ERIC P.O. Box 176 22100 Lund Sweden +46 721792250
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
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11
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Zhang C, Codina N, Tang J, Yu H, Chakroun N, Kozielski F, Dalby PA. Comparison of the pH- and thermally-induced fluctuations of a therapeutic antibody Fab fragment by molecular dynamics simulation. Comput Struct Biotechnol J 2021; 19:2726-2741. [PMID: 34093988 PMCID: PMC8131956 DOI: 10.1016/j.csbj.2021.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/15/2021] [Accepted: 05/01/2021] [Indexed: 11/27/2022] Open
Abstract
Successful development of protein therapeutics depends critically on achieving stability under a range of conditions. A deeper understanding of the drivers of instability across different stress conditions, will enable the engineering of more robust protein scaffolds. We compared the impacts of low pH and high temperature stresses on the structure of a humanized antibody fragment (Fab) A33, using atomistic molecular dynamics simulations, using a recent 2.5 Å crystal structure. This revealed that low-pH induced the loss of native contacts in the domain CL. By contrast, thermal stress led to 5-7% loss of native contacts in all four domains, and simultaneous loss of >30% of native contacts in the VL-VH and CL-CH interfaces. This revealed divergent destabilising pathways under the two different stresses. The underlying cause of instability was probed using FoldX and Rosetta mutation analysis, and packing density calculations. These agreed that mutations in the CL domain, and CL-CH1 interface have the greatest potential for stabilisation of Fab A33. Several key salt bridge losses underpinned the conformational change in CL at low pH, whereas at high temperature, salt bridges became more dynamic, thus contributing to an overall destabilization. Lastly, the unfolding events at the two stress conditions exposed different predicted aggregation-prone regions (APR) to solvent, which would potentially lead to different aggregation mechanisms. Overall, our results identified the early stages of unfolding and stability-limiting regions of Fab A33, and the VH and CL domains as interesting future targets for engineering stability to both pH- and thermal-stresses simultaneously.
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Affiliation(s)
- Cheng Zhang
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1E 7JE, United Kingdom
| | - Nuria Codina
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1E 7JE, United Kingdom
| | - Jiazhi Tang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Haoran Yu
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Nesrine Chakroun
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1E 7JE, United Kingdom
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1E 7JE, United Kingdom
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12
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Rogstam A, Nyblom M, Christensen S, Sele C, Talibov VO, Lindvall T, Rasmussen AA, André I, Fisher Z, Knecht W, Kozielski F. Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2. Int J Mol Sci 2020; 21:ijms21197375. [PMID: 33036230 PMCID: PMC7583907 DOI: 10.3390/ijms21197375] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 01/18/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), causing Coronavirus Disease 19 (COVID-19), emerged at the end of 2019 and quickly spread to cause a global pandemic with severe socio-economic consequences. The early sequencing of its RNA genome revealed its high similarity to SARS, likely to have originated from bats. The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3'-to-5' exoribonuclease and the 2'-O-methlytransferase activities of nsps 14 and 16, respectively. Here, we report the biophysical characterization and 1.6 Å resolution structure of the unbound form of nsp10 from SARS-CoV-2 and compare it to the structures of its SARS homologue and the complex-bound form with nsp16 from SARS-CoV-2. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication-transcription complex and virus replication.
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Affiliation(s)
- Annika Rogstam
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
| | - Maria Nyblom
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
| | - Signe Christensen
- Department of Biochemistry and Structural Biology, Lund University, Naturvetarvägen 26, 22241 Lund, Sweden; (S.C.); (I.A.)
| | - Celeste Sele
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
| | | | - Therese Lindvall
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
| | - Anna Andersson Rasmussen
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
| | - Ingemar André
- Department of Biochemistry and Structural Biology, Lund University, Naturvetarvägen 26, 22241 Lund, Sweden; (S.C.); (I.A.)
| | - Zoë Fisher
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
- Scientific Activities Division, Science Directorate, European Spallation Source ERIC, Box 176, SE-221 00 Lund, Sweden
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (A.R.); (M.N.); (C.S.); (T.L.); (A.A.R.); (Z.F.); (W.K.)
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- Correspondence:
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13
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Indorato RL, Talapatra SK, Lin F, Haider S, Mackay SP, Kozielski F, Skoufias DA. Is the Fate of Clinical Candidate Arry-520 Already Sealed? Predicting Resistance in Eg5–Inhibitor Complexes. Mol Cancer Ther 2019; 18:2394-2406. [DOI: 10.1158/1535-7163.mct-19-0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/20/2019] [Accepted: 08/30/2019] [Indexed: 11/16/2022]
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14
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Talapatra SK, Penny MR, Hilton ST, Kozielski F. Design, 3D printing and validation of a novel low-cost high-capacity sitting-drop bridge for protein crystallization. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576718017545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Sitting-drop protein crystallization is not used as commonly as the hanging-drop method for crystal optimization owing to the limitations of commercially available sitting-drop bridges, particularly when they are used in conjunction with 24-well crystallization plates. The commercially available sitting-drop bridge, containing space for only a single drop, restricts their wider use. Proteins that preferentially crystallize under sitting-drop conditions therefore require more work, time and resources for their optimization. In response to these limitations, and using 3D printing, a new sitting-drop bridge has been designed and developed, where five crystallization drops can be placed simultaneously in each well of a 24-well crystallization plate. This significantly simplifies the process and increases the potential of sitting drops in crystal optimization, reducing costs and hence overcoming the limitations of current approaches.
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15
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Riccio F, Talapatra SK, Oxenford S, Angell R, Mazzon M, Kozielski F. Development and validation of RdRp Screen, a crystallization screen for viral RNA-dependent RNA polymerases. Biol Open 2019; 8:8/1/bio037663. [PMID: 30602529 PMCID: PMC6361211 DOI: 10.1242/bio.037663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Members of the Flaviviridae family constitute a severe risk to human health. Whilst effective drugs have been developed against the hepacivirus HCV, no antiviral therapy is currently available for any other viruses, including the flaviviruses dengue (DENV), West Nile and Zika viruses. The RNA-dependent RNA polymerase (RdRp) is responsible for viral replication and represents an excellent therapeutic target with no homologue found in mammals. The identification of compounds targeting the RdRp of other flaviviruses is an active area of research. One of the main factors hampering further developments in the field is the difficulty in obtaining high-quality crystal information that could aid a structure-based drug discovery approach. To address this, we have developed a convenient and economical 96-well screening platform. We validated the screen by successfully obtaining crystals of both native DENV serotype 2 and 3 RdRps under several conditions included in the screen. In addition, we have obtained crystal structures of RdRp3 in complex with a previously identified fragment using both soaking and co-crystallization techniques. This work will streamline and accelerate the generation of crystal structures of viral RdRps and provide the community with a valuable tool to aid the development of structure-based antiviral design. Summary: We have developed a 96-well crystallization screen for viral RNA-dependent RNA polymerases (RdRps). The screen provides a convenient platform for streamlining the crystallisation of RdRps and implementing structure-based drug discovery programs.
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Affiliation(s)
- Federica Riccio
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Sandeep K Talapatra
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Sally Oxenford
- Translational Research Office, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Richard Angell
- Translational Research Office, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Michela Mazzon
- UCL MRC Laboratory for Molecular Cell Biology, Gower Street, London, WC1E 6BT, United Kingdom
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
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16
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Khathi SP, Chandrasekaran B, Karunanidhi S, Tham CL, Kozielski F, Sayyad N, Karpoormath R. Design and synthesis of novel thiadiazole-thiazolone hybrids as potential inhibitors of the human mitotic kinesin Eg5. Bioorg Med Chem Lett 2018; 28:2930-2938. [DOI: 10.1016/j.bmcl.2018.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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17
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Talapatra SK, Tham CL, Guglielmi P, Cirilli R, Chandrasekaran B, Karpoormath R, Carradori S, Kozielski F. Crystal structure of the Eg5 - K858 complex and implications for structure-based design of thiadiazole-containing inhibitors. Eur J Med Chem 2018; 156:641-651. [DOI: 10.1016/j.ejmech.2018.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/20/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
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18
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Georgakopoulos ND, Talapatra SK, Gatliff J, Kozielski F, Wells G. Modified Peptide Inhibitors of the Keap1-Nrf2 Protein-Protein Interaction Incorporating Unnatural Amino Acids. Chembiochem 2018; 19:1810-1816. [PMID: 29927029 PMCID: PMC6220877 DOI: 10.1002/cbic.201800170] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Indexed: 11/12/2022]
Abstract
Noncovalent inhibitors of the Keap1-Nrf2 protein-protein interaction (PPI) have therapeutic potential in a range of disease states including neurodegenerative diseases (Parkinson's and Alzheimer's diseases), chronic obstructive pulmonary disease and various inflammatory conditions. By stalling Keap1-mediated ubiquitination of Nrf2, such compounds can enhance Nrf2 transcriptional activity and activate the expression of a range of genes with antioxidant response elements in their promoter regions. Keap1 inhibitors based on peptide and small-molecule templates have been identified. In this paper we develop the structure-activity relationships of the peptide series and identify a group of ligands incorporating unnatural amino acids that demonstrate improved binding affinity in fluorescence polarisation, differential scanning fluorimetry and isothermal titration calorimetry assays. These modified peptides have the potential for further development into peptidomimetic chemical probes to explore the role of Nrf2 in disease and as potential lead structures for drug development.
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Affiliation(s)
| | - Sandeep K Talapatra
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK
| | - Jemma Gatliff
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK
| | - Frank Kozielski
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK
| | - Geoff Wells
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK
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19
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Chatrin C, Talapatra SK, Canard B, Kozielski F. The structure of the binary methyltransferase-SAH complex from Zika virus reveals a novel conformation for the mechanism of mRNA capping. Oncotarget 2017; 9:3160-3171. [PMID: 29423037 PMCID: PMC5790454 DOI: 10.18632/oncotarget.23223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/15/2017] [Indexed: 11/25/2022] Open
Abstract
Zika virus, a flavivirus like Dengue and West Nile viruses, poses a significant risk as a pathogen in the category of emerging infectious diseases. Zika infections typically cause nonspecific, mild symptoms, but can also manifest as a neurological disorder like Guillain-Barré syndrome. Infection in pregnant women is linked to microcephaly in newborn infants. The methyltransferase domain of the non-structural protein 5 is responsible for two sequential methylations of the 5′-RNA cap. This is crucial for genome stability, efficient translation, and escape from the host immune response. Here we present the crystal structures of the Zika methyltransferase domain in complex with the methyl-donor SAM and its by-product SAH. The methyltransferase-SAH binary complex presents a new conformation of a “closed” or “obstructed” state that would restrict the binding of new RNA for capping. The combination and comparison of our new structures with recently published Zika methyltransferase structures provide a first glimpse into the structural mechanism of Zika virus mRNA capping.
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Affiliation(s)
- Chatrin Chatrin
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX, London, United Kingdom
| | - Sandeep K Talapatra
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX, London, United Kingdom
| | - Bruno Canard
- CNRS, Aix Marseille University, AFMB UMR7257, Marseille, France
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX, London, United Kingdom
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20
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Balakumar C, Ramesh M, Tham CL, Khathi SP, Kozielski F, Srinivasulu C, Hampannavar GA, Sayyad N, Soliman ME, Karpoormath R. Ligand- and structure-based in silico studies to identify kinesin spindle protein (KSP) inhibitors as potential anticancer agents. J Biomol Struct Dyn 2017; 36:3687-3704. [DOI: 10.1080/07391102.2017.1396255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chandrasekaran Balakumar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Muthusamy Ramesh
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Chuin Lean Tham
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London, 29-39, Brunswick Square, London WC1N 1AX, UK
| | - Samukelisiwe Pretty Khathi
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London, 29-39, Brunswick Square, London WC1N 1AX, UK
| | - Cherukupalli Srinivasulu
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Girish A. Hampannavar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Nisar Sayyad
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Mahmoud E. Soliman
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Rajshekhar Karpoormath
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
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21
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Talapatra SK, Rath O, Clayton E, Tomasi S, Kozielski F. Depsidones from Lichens as Natural Product Inhibitors of M-Phase Phosphoprotein 1, a Human Kinesin Required for Cytokinesis. J Nat Prod 2016; 79:1576-1585. [PMID: 27300079 DOI: 10.1021/acs.jnatprod.5b00962] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
M-Phase Phosphoprotein 1 (MPP1), a microtubule plus end directed kinesin, is required for the completion of cytokinesis. Previous studies have shown that MPP1 is upregulated in various types of bladder cancer. This article describes inhibitor screening leading to the identification of a new class of natural product inhibitors of MPP1. Two compounds with structural similarity, norlobaridone (1) and physodic acid (2), were found to inhibit MPP1. Physodic acid is not competitive with ATP, indicating the presence of an allosteric inhibitor-binding pocket. Initial drug-like property screening indicates that physodic acid is more soluble than norlobaridone and has more favorable lipophilicity. However, both suffer from high clearance in human microsomal stability assays mediated by the lability of the lactone ring as well as hydroxylation of the alkyl chains as shown by metabolite identification studies. In cell-based assays physodic acid is a weak inhibitor with EC50 values of about 30 μM in a range of tumor cell lines. The two depsidones identified and characterized here could be used for future improvement of their activity against MPP1 and will be useful chemical probes for studying this unique molecular motor in more depth.
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Affiliation(s)
- Sandeep K Talapatra
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
- The Beatson Institute for Cancer Research , Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, U.K
| | - Oliver Rath
- The Beatson Institute for Cancer Research , Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, U.K
| | - Eddie Clayton
- Cyprotex Discovery Ltd , 15 Beech Lane, Macclesfield, Cheshire SK10 2DR, U.K
| | - Sophie Tomasi
- Equipe PNSCM "Produits Naturels - Synthèses - Chimie Médicinale", Unités Mixtes de Recherche, Centre National de la Recherche Scientifique, 6226 Sciences Chimiques de Rennes, UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire , 2 Avenue du Pr. Léon Bernard, F-35043 Rennes, France
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
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22
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Labrière C, Talapatra SK, Thoret S, Bougeret C, Kozielski F, Guillou C. New MKLP-2 inhibitors in the paprotrain series: Design, synthesis and biological evaluations. Bioorg Med Chem 2015; 24:721-34. [PMID: 26778612 DOI: 10.1016/j.bmc.2015.12.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/17/2015] [Accepted: 12/23/2015] [Indexed: 11/17/2022]
Abstract
Members of the kinesin superfamily are involved in key functions during intracellular transport and cell division. Their involvement in cell division makes certain kinesins potential targets for drug development in cancer chemotherapy. The two most advanced kinesin targets are Eg5 and CENP-E with inhibitors in clinical trials. Other mitotic kinesins are also being investigated for their potential as prospective drug targets. One recently identified novel potential cancer therapeutic target is the Mitotic kinesin-like protein 2 (MKLP-2), a member of the kinesin-6 family, which plays an essential role during cytokinesis. Previous studies have shown that inhibition of MKLP-2 leads to binucleated cells due to failure of cytokinesis. We have previously identified compound 1 (paprotrain) as the first selective inhibitor of MKLP-2. Herein we describe the synthesis and biological evaluation of new analogs of 1. Our structure-activity relationship (SAR) study reveals the key chemical elements in the paprotrain family necessary for MKLP-2 inhibition. We have successfully identified one MKLP-2 inhibitor 9a that is more potent than paprotrain. In addition, in vitro analysis of a panel of kinesins revealed that this compound is selective for MKLP-2 compared to other kinesins tested and also does not have an effect on microtubule dynamics. Upon testing in different cancer cell lines, we find that the more potent paprotrain analog is also more active than paprotrain in 10 different cancer cell lines. Increased selectivity and higher potency is therefore a step forward toward establishing MKLP-2 as a potential cancer drug target.
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Affiliation(s)
- Christophe Labrière
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Sandeep K Talapatra
- School of Pharmacy, University College London, Department of Pharmaceutical and Biological Chemistry, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Sylviane Thoret
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | | | - Frank Kozielski
- School of Pharmacy, University College London, Department of Pharmaceutical and Biological Chemistry, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Catherine Guillou
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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23
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Klejnot M, Falnikar A, Ulaganathan V, Cross RA, Baas PW, Kozielski F. The crystal structure and biochemical characterization of Kif15: a bifunctional molecular motor involved in bipolar spindle formation and neuronal development. ACTA ACUST UNITED AC 2013; 70:123-33. [PMID: 24419385 PMCID: PMC3919264 DOI: 10.1107/s1399004713028721] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/18/2013] [Indexed: 12/04/2022]
Abstract
The structural and biochemical study of Kif15 provides insight into this potential drug target and allows comparison with Eg5, a kinesin that partially shares the functions of Kif15. Kinesins constitute a superfamily of microtubule-based motor proteins with important cellular functions ranging from intracellular transport to cell division. Some kinesin family members function during the mitotic phase of the eukaryotic cell cycle and are crucial for the successful progression of cell division. In the early stages of mitosis, during prometaphase, certain kinesins are required for the formation of the bipolar spindle, such as Eg5 and Kif15, which seem to possess partially overlapping functions. Because kinesins transform the chemical energy from ATP hydrolysis into mechanical work, inhibition of their function is a tractable approach for drug development. Drugs targeting Eg5 have shown promise as anticancer agents. Kif15 has recently come to the fore because it can substitute the functions of Eg5, and may itself have potential as a prospective drug target. Here, the initial biochemical, kinetic and structural characterization of Kif15 is reported and it is compared with the functionally related motor Eg5. Although Kif15 contains ADP in the catalytic site, its motor-domain structure was captured in the ‘ATP-like’ configuration, with the neck linker docked to the catalytic core. The interaction of Kif15 with microtubules was also investigated and structural differences between these two motors were elucidated which indicate profound differences in their mode of action, in agreement with current models of microtubule cross-linking and sliding.
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Affiliation(s)
- Marta Klejnot
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland
| | - Aditi Falnikar
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA 19129, USA
| | | | - Robert A Cross
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, England
| | - Peter W Baas
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA 19129, USA
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, England
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24
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Talapatra SK, Anthony NG, Mackay SP, Kozielski F. Mitotic kinesin Eg5 overcomes inhibition to the phase I/II clinical candidate SB743921 by an allosteric resistance mechanism. J Med Chem 2013; 56:6317-29. [PMID: 23875972 DOI: 10.1021/jm4006274] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Development of drug resistance during cancer chemotherapy is one of the major causes of chemotherapeutic failure for the majority of clinical agents. The aim of this study was to investigate the underlying molecular mechanism of resistance developed by the mitotic kinesin Eg5 against the potent second-generation ispinesib analogue SB743921 (1), a phase I/II clinical candidate. Biochemical and biophysical data demonstrate that point mutations in the inhibitor-binding pocket decrease the efficacy of 1 by several 1000-fold. Surprisingly, the structures of wild-type and mutant Eg5 in complex with 1 display no apparent structural changes in the binding configuration of the drug candidate. Furthermore, ITC and modeling approaches reveal that resistance to 1 is not through conventional steric effects at the binding site but through reduced flexibility and changes in energy fluctuation pathways through the protein that influence its function. This is a phenomenon we have called "resistance by allostery".
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Affiliation(s)
- Sandeep K Talapatra
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BS, Scotland, U.K.
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25
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Klejnot M, Gabrielsen M, Cameron J, Mleczak A, Talapatra SK, Kozielski F, Pannifer A, Olson MF. Analysis of the human cofilin 1 structure reveals conformational changes required for actin binding. Acta Crystallogr D Biol Crystallogr 2013; 69:1780-8. [PMID: 23999301 DOI: 10.1107/s0907444913014418] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/24/2013] [Indexed: 11/10/2022]
Abstract
The actin cytoskeleton is the chassis that gives a cell its shape and structure, and supplies the power for numerous dynamic processes including motility, endocytosis, intracellular transport and division. To perform these activities, the cytoskeleton undergoes constant remodelling and reorganization. One of the major actin-remodelling families are the cofilin proteins, made up of cofilin 1, cofilin 2 and actin-depolymerizing factor (ADF), which sever aged ADP-associated actin filaments to reduce filament length and provide new potential nucleation sites. Despite the significant interest in cofilin as a central node in actin-cytoskeleton dynamics, to date the only forms of cofilin for which crystal structures have been solved are from the yeast, Chromalveolata and plant kingdoms; none have previously been reported for an animal cofilin protein. Two distinct regions in animal cofilin are significantly larger than in the forms previously crystallized, suggesting that they would be uniquely organized. Therefore, it was sought to determine the structure of human cofilin 1 by X-ray crystallography to elucidate how it could interact with and regulate dynamic actin-cytoskeletal structures. Although wild-type human cofilin 1 proved to be recalcitrant, a C147A point mutant yielded crystals that diffracted to 2.8 Å resolution. These studies revealed how the actin-binding helix undergoes a conformational change that increases the number of potential hydrogen bonds available for substrate binding.
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Affiliation(s)
- Marta Klejnot
- Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland
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26
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Kaan HYK, Major J, Tkocz K, Kozielski F, Rosenfeld SS. "Snapshots" of ispinesib-induced conformational changes in the mitotic kinesin Eg5. J Biol Chem 2013; 288:18588-98. [PMID: 23658017 DOI: 10.1074/jbc.m113.462648] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinesins comprise a superfamily of molecular motors that drive a wide variety of cellular physiologies, from cytoplasmic transport to formation of the bipolar spindle in mitosis. These differing roles are reflected in corresponding polymorphisms in key kinesin structural elements. One of these is a unique loop and stem motif found in all kinesins and referred to as loop 5 (L5). This loop is longest in the mitotic kinesin Eg5 and is the target for a number of small molecule inhibitors, including ispinesib, which is being used in clinical trials in patients with cancer. In this study, we have used x-ray crystallography to identify a new structure of an Eg5-ispinesib complex and have combined this with transient state kinetics to identify a plausible sequence of conformational changes that occur in response to ispinesib binding. Our results demonstrate that ispinesib-induced structural changes in L5 from Eg5 lead to subsequent changes in the conformation of the switch II loop and helix and in the neck linker. We conclude that L5 in Eg5 simultaneously regulates the structure of both the ATP binding site and the motor's mechanical elements that generate force.
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Affiliation(s)
- Hung Yi Kristal Kaan
- Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, United Kingdom
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27
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Good JAD, Wang F, Rath O, Kaan HYK, Talapatra SK, Podgórski D, MacKay SP, Kozielski F. Optimized S-trityl-L-cysteine-based inhibitors of kinesin spindle protein with potent in vivo antitumor activity in lung cancer xenograft models. J Med Chem 2013; 56:1878-93. [PMID: 23394180 PMCID: PMC3759169 DOI: 10.1021/jm3014597] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The mitotic kinesin Eg5 is critical
for the assembly of the mitotic
spindle and is a promising chemotherapy target. Previously, we identified S-trityl-l-cysteine as a selective inhibitor of
Eg5 and developed triphenylbutanamine analogues with improved potency,
favorable drug-like properties, but moderate in vivo activity. We
report here their further optimization to produce extremely potent
inhibitors of Eg5 (Kiapp <
10 nM) with broad-spectrum activity against cancer cell lines comparable
to the Phase II drug candidates ispinesib and SB-743921. They have
good oral bioavailability and pharmacokinetics and induced complete
tumor regression in nude mice explanted with lung cancer patient xenografts.
Furthermore, they display fewer liabilities with CYP-metabolizing
enzymes and hERG compared with ispinesib and SB-743921, which is important
given the likely application of Eg5 inhibitors in combination therapies.
We present the case for this preclinical series to be investigated
in single and combination chemotherapies, especially targeting hematological
malignancies.
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Affiliation(s)
- James A D Good
- Molecular Motors Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK.
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28
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Ulaganathan V, Talapatra SK, Rath O, Pannifer A, Hackney DD, Kozielski F. Structural insights into a unique inhibitor binding pocket in kinesin spindle protein. J Am Chem Soc 2013; 135:2263-72. [PMID: 23305346 DOI: 10.1021/ja310377d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human kinesin Eg5 is a target for drug development in cancer chemotherapy with compounds in phase II clinical trials. These agents bind to a well-characterized allosteric pocket involving the loop L5 region, a structural element in kinesin-5 family members thought to provide inhibitor specificity. Using X-ray crystallography, kinetic, and biophysical methods, we have identified and characterized a distinct allosteric pocket in Eg5 able to bind inhibitors with nanomolar K(d). This pocket is formed by key structural elements thought to be pivotal for force generation in kinesins and may represent a novel site for therapeutic intervention in this increasingly well-validated drug target.
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Affiliation(s)
- Venkatasubramanian Ulaganathan
- The Molecular Motors Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK
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29
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Talapatra SK, Schüttelkopf AW, Kozielski F. The structure of the ternary Eg5-ADP-ispinesib complex. Acta Crystallogr D Biol Crystallogr 2012; 68:1311-9. [PMID: 22993085 PMCID: PMC3447400 DOI: 10.1107/s0907444912027965] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 06/20/2012] [Indexed: 11/17/2022]
Abstract
The human kinesin Eg5 is responsible for bipolar spindle formation during early mitosis. Inhibition of Eg5 triggers the formation of monoastral spindles, leading to mitotic arrest that eventually causes apoptosis. There is increasing evidence that Eg5 constitutes a potential drug target for the development of cancer chemotherapeutics. The most advanced Eg5-targeting agent is ispinesib, which exhibits potent antitumour activity and is currently in multiple phase II clinical trials. In this study, the crystal structure of the Eg5 motor domain in complex with ispinesib, supported by kinetic and thermodynamic binding data, is reported. Ispinesib occupies the same induced-fit pocket in Eg5 as other allosteric inhibitors, making extensive hydrophobic interactions with the protein. The data for the Eg5-ADP-ispinesib complex suffered from pseudo-merohedral twinning and revealed translational noncrystallographic symmetry, leading to challenges in data processing, space-group assignment and structure solution as well as in refinement. These complications may explain the lack of available structural information for this important agent and its analogues. The present structure represents the best interpretation of these data based on extensive data-reduction, structure-solution and refinement trials.
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Affiliation(s)
- S. K. Talapatra
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - A. W. Schüttelkopf
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - F. Kozielski
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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30
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Abstract
Kinesins are a family of molecular motors that travel unidirectionally along microtubule tracks to fulfil their many roles in intracellular transport or cell division. Over the past few years kinesins that are involved in mitosis have emerged as potential targets for cancer drug development. Several compounds that inhibit two mitotic kinesins (EG5 (also known as KIF11) and centromere-associated protein E (CENPE)) have entered Phase I and II clinical trials either as monotherapies or in combination with other drugs. Additional mitotic kinesins are currently being validated as drug targets, raising the possibility that the range of kinesin-based drug targets may expand in the future.
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Affiliation(s)
- Oliver Rath
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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31
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Nagarajan S, Skoufias DA, Kozielski F, Pae AN. Receptor–Ligand Interaction-Based Virtual Screening for Novel Eg5/Kinesin Spindle Protein Inhibitors. J Med Chem 2012; 55:2561-73. [DOI: 10.1021/jm201290v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shanthi Nagarajan
- Neuro-Medicine Center, Life
Sciences Division, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Republic of Korea
- School of Science, Korea University of Science and Technology, 52 Eoeun
dongYuseong-gu, Daejeon 305-333, Republic of Korea
| | - Dimitrios A. Skoufias
- Institute for Structural Biology (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France,
| | - Frank Kozielski
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road,
Bearsden, Glasgow, G61 1BD, Scotland, U.K
| | - Ae Nim Pae
- Neuro-Medicine Center, Life
Sciences Division, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Republic of Korea
- School of Science, Korea University of Science and Technology, 52 Eoeun
dongYuseong-gu, Daejeon 305-333, Republic of Korea
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32
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Wang F, Good JAD, Rath O, Kaan HYK, Sutcliffe OB, Mackay SP, Kozielski F. Triphenylbutanamines: kinesin spindle protein inhibitors with in vivo antitumor activity. J Med Chem 2012; 55:1511-25. [PMID: 22248262 PMCID: PMC3428805 DOI: 10.1021/jm201195m] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The human mitotic kinesin Eg5 represents a novel mitotic
spindle target for cancer chemotherapy. We previously identified S-trityl-l-cysteine (STLC) and related analogues
as selective potent inhibitors of Eg5. We herein report on the development
of a series of 4,4,4-triphenylbutan-1-amine inhibitors derived from
the STLC scaffold. This new generation systematically improves on
potency: the most potent C-trityl analogues exhibit Kiapp ≤ 10 nM and GI50 ≈ 50 nM, comparable to results from the phase II clinical
benchmark ispinesib. Crystallographic studies reveal that they adopt
the same overall binding configuration as S-trityl
analogues at an allosteric site formed by loop L5 of Eg5. Evaluation
of their druglike properties reveals favorable profiles for future
development and, in the clinical candidate ispinesib, moderate hERG
and CYP inhibition. One triphenylbutanamine analogue and ispinesib
possess very good bioavailability (51% and 45%, respectively), with
the former showing in vivo antitumor growth activity in nude mice
xenograft studies.
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Affiliation(s)
- Fang Wang
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK.
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33
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Klejnot M, Kozielski F. Structural insights into human Kif7, a kinesin involved in Hedgehog signalling. Acta Crystallogr D Biol Crystallogr 2012; 68:154-9. [PMID: 22281744 PMCID: PMC3266853 DOI: 10.1107/s0907444911053042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/09/2011] [Indexed: 02/16/2023]
Abstract
The human Kif7 motor domain structure provides insights into a kinesin of medical significance. Kif7, a member of the kinesin 4 superfamily, is implicated in a variety of diseases including Joubert, hydrolethalus and acrocallosal syndromes. It is also involved in primary cilium formation and the Hedgehog signalling pathway and may play a role in cancer. Its activity is crucial for embryonic development. Kif7 and Kif27, a closely related kinesin in the same subfamily, are orthologues of the Drosophila melanogaster kinesin-like protein Costal-2 (Cos2). In vertebrates, they work together to fulfil the role of the single Cos2 gene in Drosophila. Here, the high-resolution structure of the human Kif7 motor domain is reported and is compared with that of conventional kinesin, the founding member of the kinesin superfamily. These data are a first step towards structural characterization of a kinesin-4 family member and of this interesting molecular motor of medical significance.
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Affiliation(s)
- Marta Klejnot
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland.
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34
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Nichols DB, Fournet G, Gurukumar KR, Basu A, Lee JC, Sakamoto N, Kozielski F, Musmuca I, Joseph B, Ragno R, Kaushik-Basu N. Inhibition of hepatitis C virus NS5B polymerase by S-trityl-L-cysteine derivatives. Eur J Med Chem 2012; 49:191-9. [PMID: 22280819 DOI: 10.1016/j.ejmech.2012.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 01/28/2023]
Abstract
Structure-based studies led to the identification of a constrained derivative of S-trityl-l-cysteine (STLC) scaffold as a candidate inhibitor of hepatitis C virus (HCV) NS5B polymerase. A panel of STLC derivatives were synthesized and investigated for their activity against HCV NS5B. Three STLC derivatives, 9, F-3070, and F-3065, were identified as modest HCV NS5B inhibitors with IC(50) values between 22.3 and 39.7 μM. F-3070 and F-3065 displayed potent inhibition of intracellular NS5B activity in the BHK-NS5B-FRLuc reporter and also inhibited HCV RNA replication in the Huh7/Rep-Feo1b reporter system. Binding mode investigations suggested that the STLC scaffold can be used to develop new NS5B inhibitors by further chemical modification at one of the trityl phenyl group.
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Affiliation(s)
- Daniel B Nichols
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA
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35
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Good JAD, Skoufias DA, Kozielski F. Elucidating the functionality of kinesins: an overview of small molecule inhibitors. Semin Cell Dev Biol 2011; 22:935-45. [PMID: 22001111 DOI: 10.1016/j.semcdb.2011.09.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 09/30/2011] [Indexed: 12/19/2022]
Abstract
Kinesin motor proteins are ubiquitously involved in multiple fundamental cellular processes, coordinating transport and mediating changes to cellular architecture. Thus, specific small molecule kinesin inhibitors can shed new light on the functions of kinesins and the dynamic roles in which they participate. Here we review the range of known inhibitors, their key characteristics, and specificity, and discuss their potential suitability for chemical genetics as starting points to further investigate complex kinesin-mediated processes.
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Affiliation(s)
- James A D Good
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK.
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36
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Abstract
When not transporting cargo, kinesin-1 is autoinhibited by binding of a tail region to the motor domains, but the mechanism of inhibition is unclear. We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition. Instead, the tail cross-links the motor domains at a second position, in addition to the coiled coil. This "double lockdown," by cross-linking at two positions, prevents the movement of the motor domains that is needed to undock the neck linker and release adenosine diphosphate. This autoinhibition mechanism could extend to some other kinesins.
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Affiliation(s)
- Hung Yi Kristal Kaan
- The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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37
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Kaan HYK, Weiss J, Menger D, Ulaganathan V, Tkocz K, Laggner C, Popowycz F, Joseph B, Kozielski F. Structure-activity relationship and multidrug resistance study of new S-trityl-L-cysteine derivatives as inhibitors of Eg5. J Med Chem 2011; 54:1576-86. [PMID: 21344920 DOI: 10.1021/jm100991m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The mitotic spindle is a validated target for cancer chemotherapy. Drugs such as taxanes and vinca alkaloids specifically target microtubules and cause the mitotic spindle to collapse. However, toxicity and resistance are problems associated with these drugs. Thus, alternative approaches to inhibiting the mitotic spindle are being pursued. These include targeting Eg5, a human kinesin involved in the formation of the bipolar spindle. We previously identified S-trityl-L-cysteine (STLC) as a potent allosteric inhibitor of Eg5. Here, we report the synthesis of a new series of STLC-like compounds with in vitro inhibition in the low nanomolar range. We also performed a multidrug resistance study in cell lines overexpressing P-glycoprotein and showed that some of these inhibitors may have the potential to overcome susceptibility to this efflux pump. Finally, we performed molecular docking of the compounds and determined the structures of two Eg5-inhibitor complexes to explain the structure-activity relationship of these compounds.
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Affiliation(s)
- Hung Yi Kristal Kaan
- The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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38
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Tcherniuk S, Skoufias DA, Labriere C, Rath O, Gueritte F, Guillou C, Kozielski F. Relocation of Aurora B and survivin from centromeres to the central spindle impaired by a kinesin-specific MKLP-2 inhibitor. Angew Chem Int Ed Engl 2011; 49:8228-31. [PMID: 20857469 DOI: 10.1002/anie.201003254] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sergey Tcherniuk
- IBS (CEA-CNRS-UJF), 41, rue Jules Horowitz, 38027 Grenoble, France
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39
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Tcherniuk S, Skoufias DA, Labriere C, Rath O, Gueritte F, Guillou C, Kozielski F. Relocation of Aurora B and Survivin from Centromeres to the Central Spindle Impaired by a Kinesin-Specific MKLP-2 Inhibitor. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Kaan HYK, Ulaganathan V, Rath O, Prokopcová H, Dallinger D, Kappe CO, Kozielski F. Structural basis for inhibition of Eg5 by dihydropyrimidines: stereoselectivity of antimitotic inhibitors enastron, dimethylenastron and fluorastrol. J Med Chem 2010; 53:5676-83. [PMID: 20597485 DOI: 10.1021/jm100421n] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human kinesin Eg5, which plays an essential role in mitosis by establishing the bipolar spindle, has proven to be an interesting drug target for the development of cancer chemotherapeutics. Here, we report the crystal structures of the Eg5 motor domain complexed with enastron, dimethylenastron, and fluorastrol. By comparing these structures to that of monastrol and mon-97, we identified the main reasons for increased potency of these new inhibitors, namely the better fit of the ligand to the allosteric binding site and the addition of fluorine atoms. We also noticed preferential binding of the S-enantiomer of enastron and dimethylenastron to Eg5, while the R-enantiomer of fluorastrol binds preferentially to Eg5. In addition, we performed a multidrug resistance (MDR) study in cell lines overexpressing P-glycoprotein (Pgp). We showed that one of these inhibitors may have the potential to overcome susceptibility to this efflux pump and hence overcome common resistance associated with tubulin-targeting drugs.
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Affiliation(s)
- Hung Yi Kristal Kaan
- The Beatson Institute for Cancer Research, Garscube Estate, Bearsden, Glasgow, Scotland, UK
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41
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Prokopcová H, Dallinger D, Uray G, Kaan HYK, Ulaganathan V, Kozielski F, Laggner C, Kappe CO. Structure-Activity Relationships and Molecular Docking of Novel Dihydropyrimidine-Based Mitotic Eg5 Inhibitors. ChemMedChem 2010; 5:1760-9. [DOI: 10.1002/cmdc.201000252] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Koehler CJ, Strozynski M, Kozielski F, Treumann A, Thiede B. Isobaric peptide termini labeling for MS/MS-based quantitative proteomics. J Proteome Res 2009; 8:4333-41. [PMID: 19655813 DOI: 10.1021/pr900425n] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its introduction, isobaric peptide labeling has played an important role in relative quantitative comparisons of proteomes. This paper describes isobaric peptide termini labeling (IPTL), a novel approach for the identification and quantification of two differentially labeled states using MS/MS spectra. After endoproteinase Lys-C digestion, peptides were labeled at C-terminal lysine residues with either 2-methoxy-4,5-dihydro-1H-imidazole (MDHI) or with tetradeuterated MDHI-d(4). Subsequently, their N-termini were derivatized either with tetradeuterated succinic anhydride (SA-d(4)) or with SA. The mixed isotopic labeling results in isobaric masses and provided several quantification data points per peptide. The suitability of this approach is demonstrated with MS and MS/MS analyses of Lys-C digests of standard proteins. A conceptually simple quantification strategy with a dynamic range of 25 is achieved through the use of Mascot score ratios. The utility of IPTL for the analysis of proteomes was verified by comparing the well-characterized effect of the antimitotic inhibitor S-Trityl-l-Cysteine (STLC) on HeLa cells that were treated for either 24 or 48 h with the inhibitor. Many apoptosis-linked proteins were identified as being differentially regulated, confirming the suitability of IPTL for the analysis of complex proteomes.
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Tcherniuk S, van Lis R, Kozielski F, Skoufias DA. Mutations in the human kinesin Eg5 that confer resistance to monastrol and S-trityl-L-cysteine in tumor derived cell lines. Biochem Pharmacol 2009; 79:864-72. [PMID: 19896928 DOI: 10.1016/j.bcp.2009.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 01/13/2023]
Abstract
The kinesin Eg5 plays an essential role in bipolar spindle formation. A variety of structurally diverse inhibitors of the human kinesin Eg5, including monastrol and STLC, share the same binding pocket on Eg5, composed by helix alpha2/loop L5, and helix alpha3 of the Eg5 motor domain. Previous biochemical analysis in the inhibitor binding pocket of Eg5 identified key residues in the inhibitor binding pocket of Eg5 that in the presence of either monastrol or STLC exhibited ATPase activities similar to the untreated wild type Eg5. Here we evaluated the ability of full-length human Eg5 carrying point mutations in the drug binding pocket to confer resistance in HeLa and U2OS cells to either monastrol or STLC, as measured by the formation of bipolar spindles. Both transfected cells expressing wild type Eg5 and untransfected cells were equally sensitive to both inhibitors. Expression of Eg5 single point mutants R119A, D130A, L132A, I136A, L214A and E215A conferred significant resistance to monastrol. Certain mutations inducing monastrol resistance such as R119A, D130A and L214A also conferred significant resistance to STLC. For the first time at a cellular level, the propensity of selected Eg5 point mutants to confer drug resistance confirms the target specificity of monastrol and STLC for Eg5. These data also suggest a possible mechanism by which drug resistance may occur in tumors treated with agents targeting Eg5.
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Affiliation(s)
- Sergey Tcherniuk
- Institut de Biologie Structurale, (CEA-CNRS-UJF) J.P.Ebel, Laboratoire des Protéines du Cytosquelette 41 rue Jules Horowitz, 38027 Grenoble Cedex 01, France
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Putey A, Popowycz F, Do QT, Bernard P, Talapatra SK, Kozielski F, Galmarini CM, Joseph B. Indolobenzazepin-7-ones and 6-, 8-, and 9-Membered Ring Derivatives as Tubulin Polymerization Inhibitors: Synthesis and Structure−Activity Relationship Studies. J Med Chem 2009; 52:5916-25. [DOI: 10.1021/jm900476c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aurélien Putey
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR-CNRS 5246, Laboratoire de Chimie Organique 1, Université de Lyon, Université Claude Bernard-Lyon 1, Bâtiment Curien, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Florence Popowycz
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR-CNRS 5246, Laboratoire de Chimie Organique 1, Université de Lyon, Université Claude Bernard-Lyon 1, Bâtiment Curien, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Quoc-Tuan Do
- GreenPharma SA, 3 Allée du Titane, 45100 Orléans, France
| | | | - Sandeep K. Talapatra
- The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, U.K
| | - Frank Kozielski
- The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, U.K
| | - Carlos M. Galmarini
- ENS-CNRS UMR 5239, UFR de Médecine Lyon-Sud, 165 chemin du Grand Revoyet, BP 12, 69921 Oullins, France
| | - Benoît Joseph
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR-CNRS 5246, Laboratoire de Chimie Organique 1, Université de Lyon, Université Claude Bernard-Lyon 1, Bâtiment Curien, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne, France
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Peris L, Wagenbach M, Lafanechère L, Brocard J, Moore AT, Kozielski F, Job D, Wordeman L, Andrieux A. Motor-dependent microtubule disassembly driven by tubulin tyrosination. ACTA ACUST UNITED AC 2009; 185:1159-66. [PMID: 19564401 PMCID: PMC2712961 DOI: 10.1083/jcb.200902142] [Citation(s) in RCA: 242] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In cells, stable microtubules (MTs) are covalently modified by a carboxypeptidase, which removes the C-terminal Tyr residue of α-tubulin. The significance of this selective detyrosination of MTs is not understood. In this study, we report that tubulin detyrosination in fibroblasts inhibits MT disassembly. This inhibition is relieved by overexpression of the depolymerizing motor mitotic centromere-associated kinesin (MCAK). Conversely, suppression of MCAK expression prevents disassembly of normal tyrosinated MTs in fibroblasts. Detyrosination of MTs suppresses the activity of MCAK in vitro, apparently as the result of a decreased affinity of the adenosine diphosphate (ADP)–inorganic phosphate- and ADP-bound forms of MCAK for the MT lattice. Detyrosination also impairs MT disassembly in neurons and inhibits the activity of the neuronal depolymerizing motor KIF2A in vitro. These results indicate that MT depolymerizing motors are directly inhibited by the detyrosination of tubulin, resulting in the stabilization of cellular MTs. Detyrosination of transiently stabilized MTs may give rise to persistent subpopulations of disassembly-resistant polymers to sustain subcellular cytoskeletal differentiation.
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Affiliation(s)
- Leticia Peris
- Institut National de la Santé et de la Recherche Medicale Unité 836, Institut des Neurosciences de Grenoble, 38042 Grenoble, Cedex 9, France.
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Lopez R, Comas H, Buisson DA, Najman R, Kozielski F, Rousseau B. Synthesis of 5-Acyl-3,4-dihydropyrimidine-2-thiones via Solvent-Free, Solution-Phase and Solid-Phase Biginelli Procedures. Synlett 2009. [DOI: 10.1055/s-0029-1217373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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Popowycz F, Schneider C, DeBonis S, Skoufias DA, Kozielski F, Galmarini CM, Joseph B. Synthesis and antiproliferative evaluation of pyrazolo[1,5-a]-1,3,5-triazine myoseverin derivatives. Bioorg Med Chem 2009; 17:3471-8. [DOI: 10.1016/j.bmc.2009.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 03/02/2009] [Accepted: 03/03/2009] [Indexed: 10/21/2022]
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Debonis S, Skoufias DA, Indorato RL, Liger F, Marquet B, Laggner C, Joseph B, Kozielski F. Structure-activity relationship of S-trityl-L-cysteine analogues as inhibitors of the human mitotic kinesin Eg5. J Med Chem 2008; 51:1115-25. [PMID: 18266314 DOI: 10.1021/jm070606z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human kinesin Eg5 is a potential drug target for cancer chemotherapy. Eg5 specific inhibitors cause cells to block in mitosis with a characteristic monoastral spindle phenotype. Prolonged metaphase block eventually leads to apoptotic cell death. S-trityl-L-cysteine (STLC) is a tight-binding inhibitor of Eg5 that prevents mitotic progression. It has proven antitumor activity as shown in the NCI 60 tumor cell line screen. It is of considerable interest to define the minimum chemical structure that is essential for Eg5 inhibition and to develop more potent STLC analogues. An initial structure-activity relationship study on a series of STLC analogues reveals the minimal skeleton necessary for Eg5 inhibition as well as indications of how to obtain more potent analogues. The most effective compounds investigated with substitutions at the para-position of one phenyl ring have an estimated K i (app) of 100 nM in vitro and induce mitotic arrest with an EC 50 of 200 nM.
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Affiliation(s)
- Salvatore Debonis
- Institut de Biologie Structurale, 41, rue Jules Horowitz, 38027 Grenoble Cedex 01, France
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Kozielski F, Skoufias DA, Indorato RL, Saoudi Y, Jungblut PR, Hustoft HK, Strozynski M, Thiede B. Proteome analysis of apoptosis signaling byS-trityl-L-cysteine, a potent reversible inhibitor of human mitotic kinesin Eg5. Proteomics 2008; 8:289-300. [DOI: 10.1002/pmic.200700534] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Klein E, DeBonis S, Thiede B, Skoufias DA, Kozielski F, Lebeau L. New chemical tools for investigating human mitotic kinesin Eg5. Bioorg Med Chem 2007; 15:6474-88. [PMID: 17587586 DOI: 10.1016/j.bmc.2007.06.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 05/24/2007] [Accepted: 06/05/2007] [Indexed: 10/23/2022]
Abstract
We have designed and synthesized a series of monastrol derivatives, an allosteric inhibitor of Eg5, a motor protein responsible for the formation and maintenance of the bipolar spindle in mitotic cells. Sterically demanding structural modifications have been introduced on the skeleton of the parent drug either via a multicomponent Biginelli reaction or a stepwise modification of monastrol. The ability of these compounds to inhibit Eg5 activity has been investigated using two in vitro steady-state ATPase assays (basal and microtubule-stimulated) as well as a cell-based assay. One compound in the series appeared more potent than monastrol by a fivefold factor. Three other compounds that were unable to inhibit Eg5 ATPase activity in vitro proved potent Eg5 inhibitors in the cell-based assay. The results obtained led to the identification of structure-activity relationships further used to design an affinity matrix that can be used for fast and efficient purification of Eg5 from crude lysate of eukaryotic cells.
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Affiliation(s)
- Emmanuel Klein
- Institut Gilbert-Laustriat, CNRS-Université Louis Pasteur, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
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