1
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Champiré A, Berabez R, Braka A, Cosson A, Corret J, Girardin C, Serrano A, Aci-Sèche S, Bonnet P, Josselin B, Brindeau P, Ruchaud S, Leguevel R, Chatterjee D, Mathea S, Knapp S, Brion R, Verrecchia F, Vallée B, Plé K, Bénédetti H, Routier S. Tetrahydropyridine LIMK inhibitors: Structure activity studies and biological characterization. Eur J Med Chem 2024; 271:116391. [PMID: 38669909 DOI: 10.1016/j.ejmech.2024.116391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
LIM Kinases, LIMK1 and LIMK2, have become promising targets for the development of inhibitors with potential application for the treatment of several major diseases. LIMKs play crucial roles in cytoskeleton remodeling as downstream effectors of small G proteins of the Rho-GTPase family, and as major regulators of cofilin, an actin depolymerizing factor. In this article we describe the conception, synthesis, and biological evaluation of novel tetrahydropyridine pyrrolopyrimidine LIMK inhibitors. Homology models were first constructed to better understand the binding mode of our preliminary compounds and to explain differences in biological activity. A library of over 60 products was generated and in vitro enzymatic activities were measured in the mid to low nanomolar range. The most promising derivatives were then evaluated in cell on cofilin phosphorylation inhibition which led to the identification of 52 which showed excellent selectivity for LIMKs in a kinase selectivity panel. We also demonstrated that 52 affected the cell cytoskeleton by disturbing actin filaments. Cell migration studies with this derivative using three different cell lines displayed a significant effect on cell motility. Finally, the crystal structure of the kinase domain of LIMK2 complexed with 52 was solved, greatly improving our understanding of the interaction between 52 and LIMK2 active site. The reported data represent a basis for the development of more efficient LIMK inhibitors for future in vivo preclinical validation.
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Affiliation(s)
- Anthony Champiré
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France
| | - Rayan Berabez
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France
| | - Abdennour Braka
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France
| | - Aurélie Cosson
- Centre de Biophysique Moléculaire, CNRS UPR4301, 45071, Orléans, France
| | - Justine Corret
- Centre de Biophysique Moléculaire, CNRS UPR4301, 45071, Orléans, France
| | - Caroline Girardin
- Centre de Biophysique Moléculaire, CNRS UPR4301, 45071, Orléans, France
| | - Amandine Serrano
- Centre de Biophysique Moléculaire, CNRS UPR4301, 45071, Orléans, France
| | - Samia Aci-Sèche
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France
| | - Pascal Bonnet
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France
| | - Béatrice Josselin
- Sorbonne Université / CNRS UMR 8227, Station Biologique, 29688, Roscoff, France
| | - Pierre Brindeau
- Sorbonne Université / CNRS UMR 8227, Station Biologique, 29688, Roscoff, France
| | - Sandrine Ruchaud
- Sorbonne Université / CNRS UMR 8227, Station Biologique, 29688, Roscoff, France
| | - Rémy Leguevel
- Plate-forme ImPACcell, UAR BIOSIT, Université de Rennes 1, 35043, Rennes, France
| | - Deep Chatterjee
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences Goethe- University, 60438, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Goethe-University, 60438, Frankfurt am Main, Germany
| | - Sebastian Mathea
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences Goethe- University, 60438, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Goethe-University, 60438, Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences Goethe- University, 60438, Frankfurt am Main, Germany; Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Goethe-University, 60438, Frankfurt am Main, Germany
| | - Régis Brion
- CRCI(2)NA, INSERM, UMR 1307, CNRS, UMR 6075, Université de Nantes, 44035, Nantes, France; Centre Hospitalier Universitaire de Nantes, 44000, Nantes, France
| | - Franck Verrecchia
- CRCI(2)NA, INSERM, UMR 1307, CNRS, UMR 6075, Université de Nantes, 44035, Nantes, France
| | - Béatrice Vallée
- Centre de Biophysique Moléculaire, CNRS UPR4301, 45071, Orléans, France
| | - Karen Plé
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS UPR4301, 45071, Orléans, France.
| | - Sylvain Routier
- ICOA, Université d'Orléans, CNRS UMR 7311, 45067, Orléans, France.
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2
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Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. Nat Commun 2024; 15:1426. [PMID: 38365893 PMCID: PMC10873347 DOI: 10.1038/s41467-024-45878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short, unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but specific aspects driving this conservation are unclear. Here, we screen a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and biochemical analysis of individual variants reveal distinct sequence requirements for actin binding and regulation by LIM kinase. LIM kinase recognition only partly explains sequence constraints on phosphoregulation, which are instead driven to a large extent by the capacity for phosphorylation to inactivate cofilin. We find loose sequence requirements for actin binding and phosphoinhibition, but collectively they restrict the N-terminus to sequences found in natural cofilins. Our results illustrate how a phosphorylation site can balance potentially competing sequence requirements for function and regulation.
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Affiliation(s)
- Joel A Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jeffrey P Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA.
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3
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Casanova-Sepúlveda G, Sexton JA, Turk BE, Boggon TJ. Autoregulation of the LIM kinases by their PDZ domain. Nat Commun 2023; 14:8441. [PMID: 38114480 PMCID: PMC10730565 DOI: 10.1038/s41467-023-44148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
LIM domain kinases (LIMK) are important regulators of actin cytoskeletal remodeling. These protein kinases phosphorylate the actin depolymerizing factor cofilin to suppress filament severing, and are key nodes between Rho GTPase cascades and actin. The two mammalian LIMKs, LIMK1 and LIMK2, contain consecutive LIM domains and a PDZ domain upstream of the C-terminal kinase domain. The roles of the N-terminal regions are not fully understood, and the function of the PDZ domain remains elusive. Here, we determine the 2.0 Å crystal structure of the PDZ domain of LIMK2 and reveal features not previously observed in PDZ domains including a core-facing arginine residue located at the second position of the 'x-Φ-G-Φ' motif, and that the expected peptide binding cleft is shallow and poorly conserved. We find a distal extended surface to be highly conserved, and when LIMK1 was ectopically expressed in yeast we find targeted mutagenesis of this surface decreases growth, implying increased LIMK activity. PDZ domain LIMK1 mutants expressed in yeast are hyperphosphorylated and show elevated activity in vitro. This surface in both LIMK1 and LIMK2 is critical for autoregulation independent of activation loop phosphorylation. Overall, our study demonstrates the functional importance of the PDZ domain to autoregulation of LIMKs.
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Affiliation(s)
| | - Joel A Sexton
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA.
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4
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Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547189. [PMID: 37425676 PMCID: PMC10327202 DOI: 10.1101/2023.06.30.547189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but the aspects of cofilin functionality driving this conservation are not clear. Here, we screened a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and subsequent biochemical analysis of individual variants revealed distinct sequence requirements for actin binding and regulation by LIM kinase. While the presence of a serine, rather than threonine, phosphoacceptor residue was essential for phosphorylation by LIM kinase, the native cofilin N-terminus was otherwise a suboptimal LIM kinase substrate. This circumstance was not due to sequence requirements for actin binding and severing, but rather appeared primarily to maintain the capacity for phosphorylation to inactivate cofilin. Overall, the individual sequence requirements for cofilin function and regulation were remarkably loose when examined separately, but collectively restricted the N-terminus to sequences found in natural cofilins. Our results illustrate how a regulatory phosphorylation site can balance potentially competing sequence requirements for function and regulation.
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Affiliation(s)
- Joel A. Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jeffrey P. Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Enrique M. De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
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5
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Shah K, Cook M. LIMK2: A Multifaceted kinase with pleiotropic roles in human physiology and pathologies. Cancer Lett 2023; 565:216207. [PMID: 37141984 PMCID: PMC10316521 DOI: 10.1016/j.canlet.2023.216207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
LIMK2, a serine-specific kinase, was discovered as an actin dynamics regulating kinase. Emerging studies have shown its pivotal role in numerous human malignancies and neurodevelopmental disorder. Inducible knockdown of LIMK2 fully reverses tumorigenesis, underscoring its potential as a clinical target. However, the molecular mechanisms leading to its upregulation and its deregulated activity in various diseases largely remain unknown. Similarly, LIMK2's peptide substrate specificity has not been analyzed. This is particularly important for LIMK2, a kinase almost three decades old, as only a handful of its substrates are known to date. As a result, most of LIMK2's physiological and pathological roles have been assigned to its regulation of actin dynamics via cofilin. This review focuses on LIMK2's unique catalytic mechanism, substrate specificity and its upstream regulators at transcriptional, post-transcriptional and post-translational stages. Moreover, emerging studies have unveiled a few tumor suppressors and oncogenes as LIMK2's direct substrates, which in turn have uncovered novel molecular mechanisms by which it plays pleiotropic roles in human physiology and pathologies independent of actin dynamics.
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Affiliation(s)
- Kavita Shah
- Department of Chemistry and Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA.
| | - Mason Cook
- Department of Chemistry and Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA
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6
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Collins R, Lee H, Jones DH, Elkins JM, Gillespie JA, Thomas C, Baldwin AG, Jones K, Waters L, Paine M, Atack JR, Ward SE, Grubisha O, Foley DW. Comparative Analysis of Small-Molecule LIMK1/2 Inhibitors: Chemical Synthesis, Biochemistry, and Cellular Activity. J Med Chem 2022; 65:13705-13713. [PMID: 36205722 PMCID: PMC9619402 DOI: 10.1021/acs.jmedchem.2c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Indexed: 11/30/2022]
Abstract
LIM domain kinases 1 and 2 (LIMK1 and LIMK2) regulate actin dynamics and subsequently key cellular functions such as proliferation and migration. LIMK1 and LIMK2 phosphorylate and inactivate cofilin leading to increased actin polymerization. As a result, LIMK inhibitors are emerging as a promising treatment strategy for certain cancers and neurological disorders. High-quality chemical probes are required if the role of these kinases in health and disease is to be understood. To that end, we report the results of a comparative assessment of 17 reported LIMK1/2 inhibitors in a variety of in vitro enzymatic and cellular assays. Our evaluation has identified three compounds (TH-257, LIJTF500025, and LIMKi3) as potent and selective inhibitors suitable for use as in vitro and in vivo pharmacological tools for the study of LIMK function in cell biology.
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Affiliation(s)
- Ross Collins
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Hyunah Lee
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - D. Heulyn Jones
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Jonathan M. Elkins
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Jason A. Gillespie
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Carys Thomas
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Alex G. Baldwin
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Kimberley Jones
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Loren Waters
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Marie Paine
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - John R. Atack
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Simon E. Ward
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Olivera Grubisha
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - David W. Foley
- Medicines
Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
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7
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Hanke T, Mathea S, Woortman J, Salah E, Berger BT, Tumber A, Kashima R, Hata A, Kuster B, Müller S, Knapp S. Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes. J Med Chem 2022; 65:13264-13287. [PMID: 36136092 DOI: 10.1021/acs.jmedchem.2c01106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LIMKs are important regulators of actin and microtubule dynamics, and they play essential roles in many cellular processes. Deregulation of LIMKs has been linked to the development of diverse diseases, including cancers and cognitive disabilities, but well-characterized inhibitors known as chemical probes are still lacking. Here, we report the characterization of three highly selective LIMK1/2 inhibitors covering all canonical binding modes (type I/II/III) and the structure-based design of the type II/III inhibitors. Characterization of these chemical probes revealed a low nanomolar affinity for LIMK1/2, and all inhibitors 1 (LIMKi3; type I), 48 (TH470; type II), and 15 (TH257; type III) showed excellent selectivity in a comprehensive scanMAX kinase selectivity panel. Phosphoproteomics revealed remarkable differences between type I and type II inhibitors compared with the allosteric inhibitor 15. In phenotypic assays such as neurite outgrowth models of fragile X-chromosome, 15 showed promising activity, suggesting the potential application of allosteric LIMK inhibitors treating this orphan disease.
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Affiliation(s)
- Thomas Hanke
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Risa Kashima
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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8
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Monteleone S, Fedorov DG, Townsend-Nicholson A, Southey M, Bodkin M, Heifetz A. Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method. J Chem Inf Model 2022; 62:3784-3799. [PMID: 35939049 DOI: 10.1021/acs.jcim.2c00457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-protein interactions (PPIs) are essential for the function of many proteins. Aberrant PPIs have the potential to lead to disease, making PPIs promising targets for drug discovery. There are over 64,000 PPIs in the human interactome reference database; however, to date, very few PPI modulators have been approved for clinical use. Further development of PPI-specific therapeutics is highly dependent on the availability of structural data and the existence of reliable computational tools to explore the interface between two interacting proteins. The fragment molecular orbital (FMO) quantum mechanics method offers comprehensive and computationally inexpensive means of identifying the strength (in kcal/mol) and the chemical nature (electrostatic or hydrophobic) of the molecular interactions taking place at the protein-protein interface. We have integrated FMO and PPI exploration (FMO-PPI) to identify the residues that are critical for protein-protein binding (hotspots). To validate this approach, we have applied FMO-PPI to a dataset of protein-protein complexes representing several different protein subfamilies and obtained FMO-PPI results that are in agreement with published mutagenesis data. We observed that critical PPIs can be divided into three major categories: interactions between residues of two proteins (intermolecular), interactions between residues within the same protein (intramolecular), and interactions between residues of two proteins that are mediated by water molecules (water bridges). We extended our findings by demonstrating how this information obtained by FMO-PPI can be utilized to support the structure-based drug design of PPI modulators (SBDD-PPI).
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Affiliation(s)
- Stefania Monteleone
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Michelle Southey
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Michael Bodkin
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Alexander Heifetz
- Evotec UK Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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9
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Singh R, Pokle AV, Ghosh P, Ganeshpurkar A, Swetha R, Singh SK, Kumar A. Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulations study for the identification of LIM kinase-1 inhibitors. J Biomol Struct Dyn 2022:1-15. [PMID: 35862656 DOI: 10.1080/07391102.2022.2101529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
LIM kinases (LIMKs) are a family of protein kinases involved in the regulation of actin dynamics. There are two isoforms of LIMKs i.e., LIMK1 and LIMK2. LIMK1 is expressed abundantly in neuronal tissues. LIMK1 plays an essential role in the degradation of dendritic spines, which are important for our higher brain functions, such as memory and learning. The inhibition of LIMK1 improves the size and density of dendritic spines and acts as a protective effect against Alzheimer's disease. In this study, we have adopted ligand-based drug design and molecular modelling methods to identify virtual hits. The pharmacophoric features of PF-00477736 were used to screen the Zinc15 compounds library. The identified hits were then passed through drug-likeliness and PAINS filters. Further, comprehensive docking and rigorous molecular dynamics simulation study afforded three virtual hits viz., ZINC504485634, ZINC16940431 and ZINC1091071. The hits showed a better docking score than the standard ligand, PF-00477736. The docking score was found to be -8.85, -7.50 and -7.68 kcal/mol. These hits exhibited optimal binding properties with the target in docking study, blood-brain barrier permeability, in silico pharmacokinetics and low predicted toxicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Singh
- Department of Pharmaceutical Engineering & Technology, Pharmaceutical Chemistry Research Laboratory 1, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Vyankatrao Pokle
- Department of Pharmaceutical Engineering & Technology, Pharmaceutical Chemistry Research Laboratory 1, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Powsali Ghosh
- Department of Pharmaceutical Engineering & Technology, Pharmaceutical Chemistry Research Laboratory 1, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Ganeshpurkar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharti Vidyapeeth, Erandwane, Pune, India
| | - Rayala Swetha
- Department of Pharmaceutical Engineering & Technology, Pharmaceutical Chemistry Research Laboratory 1, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushil Kumar Singh
- Department of Pharmaceutical Engineering & Technology, Pharmaceutical Chemistry Research Laboratory 1, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ashok Kumar
- Department of Pharmaceutical Engineering & Technology, Pharmaceutical Chemistry Research Laboratory 1, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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10
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LIM Kinases, Promising but Reluctant Therapeutic Targets: Chemistry and Preclinical Validation In Vivo. Cells 2022; 11:cells11132090. [PMID: 35805176 PMCID: PMC9265711 DOI: 10.3390/cells11132090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
LIM Kinases are important actors in the regulation of cytoskeleton dynamics by controlling microtubule and actin filament turnover. The signaling pathways involving LIM kinases for actin filament remodeling are well established. They are downstream effectors of small G proteins of the Rho-GTPases family and have become promising targets for the treatment of several major diseases because of their position at the lower end of these signaling cascades. Cofilin, which depolymerizes actin filaments, is the best-known substrate of these enzymes. The phosphorylation of cofilin to its inactive form by LIM kinases avoids actin filament depolymerization. The balance between phosphorylated and non-phosphorylated cofilin is thought to play an important role in tumor cell invasion and metastasis. Since 2006, many small molecules have been developed for LIMK inhibition, and in this review article, we will discuss the structure–activity relationships of the few inhibitor families that have been tested in vivo on different pathological models.
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Cytoskeletal dynamics regulates stromal invasion behavior of distinct liver cancer subtypes. Commun Biol 2022; 5:202. [PMID: 35241781 PMCID: PMC8894393 DOI: 10.1038/s42003-022-03121-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/08/2022] [Indexed: 02/07/2023] Open
Abstract
Drug treatment against liver cancer has limited efficacy due to heterogeneous response among liver cancer subtypes. In addition, the functional biophysical phenotypes which arise from this heterogeneity and contribute to aggressive invasive behavior remain poorly understood. This study interrogated how heterogeneity in liver cancer subtypes contributes to differences in invasive phenotypes and drug response. Utilizing histological analysis, quantitative 2D invasion metrics, reconstituted 3D hydrogels, and bioinformatics, our study linked cytoskeletal dynamics to differential invasion profiles and drug resistance in liver cancer subtypes. We investigated cytoskeletal regulation in 2D and 3D culture environments using two liver cancer cell lines, SNU-475 and HepG2, chosen for their distinct cytoskeletal features and invasion profiles. For SNU-475 cells, a model for aggressive liver cancer, many cytoskeletal inhibitors abrogated 2D migration but only some suppressed 3D migration. For HepG2 cells, cytoskeletal inhibition did not significantly affect 3D migration but did affect proliferative capabilities and spheroid core growth. This study highlights cytoskeleton driven phenotypic variation, their consequences and coexistence within the same tumor, as well as efficacy of targeting biophysical phenotypes that may be masked in traditional screens against tumor growth. Treatment for liver cancer is complicated by its various subtypes, which show different responses to anticancer drugs. This study demonstrates the effectiveness of targeting biophysical phenotypes related to cytoskeleton properties that are usually masked in traditional drug screens.
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Ribba AS, Fraboulet S, Sadoul K, Lafanechère L. The Role of LIM Kinases during Development: A Lens to Get a Glimpse of Their Implication in Pathologies. Cells 2022; 11:cells11030403. [PMID: 35159213 PMCID: PMC8834001 DOI: 10.3390/cells11030403] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
The organization of cell populations within animal tissues is essential for the morphogenesis of organs during development. Cells recognize three-dimensional positions with respect to the whole organism and regulate their cell shape, motility, migration, polarization, growth, differentiation, gene expression and cell death according to extracellular signals. Remodeling of the actin filaments is essential to achieve these cell morphological changes. Cofilin is an important binding protein for these filaments; it increases their elasticity in terms of flexion and torsion and also severs them. The activity of cofilin is spatiotemporally inhibited via phosphorylation by the LIM domain kinases 1 and 2 (LIMK1 and LIMK2). Phylogenetic analysis indicates that the phospho-regulation of cofilin has evolved as a mechanism controlling the reorganization of the actin cytoskeleton during complex multicellular processes, such as those that occur during embryogenesis. In this context, the main objective of this review is to provide an update of the respective role of each of the LIM kinases during embryonic development.
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Chatterjee D, Preuss F, Dederer V, Knapp S, Mathea S. Structural Aspects of LIMK Regulation and Pharmacology. Cells 2022; 11:cells11010142. [PMID: 35011704 PMCID: PMC8750758 DOI: 10.3390/cells11010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Malfunction of the actin cytoskeleton is linked to numerous human diseases including neurological disorders and cancer. LIMK1 (LIM domain kinase 1) and its paralogue LIMK2 are two closely related kinases that control actin cytoskeleton dynamics. Consequently, they are potential therapeutic targets for the treatment of such diseases. In the present review, we describe the LIMK conformational space and its dependence on ligand binding. Furthermore, we explain the unique catalytic mechanism of the kinase, shedding light on substrate recognition and how LIMK activity is regulated. The structural features are evaluated for implications on the drug discovery process. Finally, potential future directions for targeting LIMKs pharmacologically, also beyond just inhibiting the kinase domain, are discussed.
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Affiliation(s)
- Deep Chatterjee
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Franziska Preuss
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Verena Dederer
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
- Correspondence:
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Bourdais A, Dehapiot B, Halet G. Cofilin regulates actin network homeostasis and microvilli length in mouse oocytes. J Cell Sci 2021; 134:273797. [PMID: 34841429 DOI: 10.1242/jcs.259237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022] Open
Abstract
How multiple actin networks coexist in a common cytoplasm while competing for a shared pool of monomers is still an ongoing question. This is exemplified by meiotic maturation in the mouse oocyte, which relies on the dynamic remodeling of distinct cortical and cytoplasmic F-actin networks. Here, we show that the conserved actin-depolymerizing factor cofilin is activated in a switch-like manner upon meiosis resumption from prophase arrest. Interfering with cofilin activation during maturation resulted in widespread elongation of microvilli, while cytoplasmic F-actin was depleted, leading to defects in spindle migration and polar body extrusion. In contrast, cofilin inactivation in metaphase II-arrested oocytes resulted in a shutdown of F-actin dynamics, along with a dramatic overgrowth of the polarized actin cap. However, inhibition of the Arp2/3 complex to promote actin cap disassembly elicited ectopic microvilli outgrowth in the polarized cortex. These data establish cofilin as a key player in actin network homeostasis in oocytes and reveal that microvilli can act as a sink for monomers upon disassembly of a competing network.
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Affiliation(s)
- Anne Bourdais
- Institut Génétique et Développement de Rennes , CNRS IGDR UMR 6290, Université de Rennes 1, F-35000 Rennes, France
| | - Benoit Dehapiot
- Institut Génétique et Développement de Rennes , CNRS IGDR UMR 6290, Université de Rennes 1, F-35000 Rennes, France
| | - Guillaume Halet
- Institut Génétique et Développement de Rennes , CNRS IGDR UMR 6290, Université de Rennes 1, F-35000 Rennes, France
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Progress in the therapeutic inhibition of Cdc42 signalling. Biochem Soc Trans 2021; 49:1443-1456. [PMID: 34100887 PMCID: PMC8286826 DOI: 10.1042/bst20210112] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Cdc42 is a member of the Rho family of small GTPases and a key regulator of the actin cytoskeleton, controlling cell motility, polarity and cell cycle progression. It signals downstream of the master regulator Ras and is essential for cell transformation by this potent oncogene. Overexpression of Cdc42 is observed in several cancers, where it is linked to poor prognosis. As a regulator of both cell architecture and motility, deregulation of Cdc42 is also linked to tumour metastasis. Like Ras, Cdc42 and other components of the signalling pathways it controls represent important potential targets for cancer therapeutics. In this review, we consider the progress that has been made targeting Cdc42, its regulators and effectors, including new modalities and new approaches to inhibition. Strategies under consideration include inhibition of lipid modification, modulation of Cdc42-GEF, Cdc42-GDI and Cdc42-effector interactions, and direct inhibition of downstream effectors.
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