1
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Jin H, Kim J, Lee O, Kim H, No KT. Leveraging the Fragment Molecular Orbital Method to Explore the PLK1 Kinase Binding Site and Polo-Box Domain for Potent Small-Molecule Drug Design. Int J Mol Sci 2023; 24:15639. [PMID: 37958623 PMCID: PMC10650754 DOI: 10.3390/ijms242115639] [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: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Polo-like kinase 1 (PLK1) plays a pivotal role in cell division regulation and emerges as a promising therapeutic target for cancer treatment. Consequently, the development of small-molecule inhibitors targeting PLK1 has become a focal point in contemporary research. The adenosine triphosphate (ATP)-binding site and the polo-box domain in PLK1 present crucial interaction sites for these inhibitors, aiming to disrupt the protein's function. However, designing potent and selective small-molecule inhibitors can be challenging, requiring a deep understanding of protein-ligand interaction mechanisms at these binding sites. In this context, our study leverages the fragment molecular orbital (FMO) method to explore these site-specific interactions in depth. Using the FMO approach, we used the FMO method to elucidate the molecular mechanisms of small-molecule drugs binding to these sites to design PLK1 inhibitors that are both potent and selective. Our investigation further entailed a comparative analysis of various PLK1 inhibitors, each characterized by distinct structural attributes, helping us gain a better understanding of the relationship between molecular structure and biological activity. The FMO method was particularly effective in identifying key binding features and predicting binding modes for small-molecule ligands. Our research also highlighted specific "hot spot" residues that played a critical role in the selective and robust binding of PLK1. These findings provide valuable insights that can be used to design new and effective PLK1 inhibitors, which can have significant implications for developing anticancer therapeutics.
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Affiliation(s)
- Haiyan Jin
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (H.J.); (O.L.)
| | - Jongwan Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
| | - Onju Lee
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (H.J.); (O.L.)
| | - Hyein Kim
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (H.J.); (O.L.)
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
- Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea
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2
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Park JE, Kirsch K, Lee H, Oliva P, Ahn JI, Ravishankar H, Zeng Y, Fox SD, Kirby SA, Badhwar P, Andresson T, Jacobson KA, Lee KS. Specific inhibition of an anticancer target, polo-like kinase 1, by allosterically dismantling its mechanism of substrate recognition. Proc Natl Acad Sci U S A 2023; 120:e2305037120. [PMID: 37603740 PMCID: PMC10629583 DOI: 10.1073/pnas.2305037120] [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: 03/28/2023] [Accepted: 07/07/2023] [Indexed: 08/23/2023] Open
Abstract
Polo-like kinase 1 (Plk1) is considered an attractive target for anticancer therapy. Over the years, studies on the noncatalytic polo-box domain (PBD) of Plk1 have raised the expectation of generating highly specific protein-protein interaction inhibitors. However, the molecular nature of the canonical PBD-dependent interaction, which requires extensive water network-mediated interactions with its phospholigands, has hampered efforts to identify small molecules suitable for Plk1 PBD drug discovery. Here, we report the identification of the first allosteric inhibitor of Plk1 PBD, called Allopole, a prodrug that can disrupt intracellular interactions between PBD and its cognate phospholigands, delocalize Plk1 from centrosomes and kinetochores, and induce mitotic block and cancer cell killing. At the structural level, its unmasked active form, Allopole-A, bound to a deep Trp-Phe-lined pocket occluded by a latch-like loop, whose adjoining region was required for securely retaining a ligand anchored to the phospho-binding cleft. Allopole-A binding completely dislodged the L2 loop, an event that appeared sufficient to trigger the dissociation of a phospholigand and inhibit PBD-dependent Plk1 function during mitosis. Given Allopole's high specificity and antiproliferative potency, this study is expected to open an unexplored avenue for developing Plk1 PBD-specific anticancer therapeutic agents.
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Affiliation(s)
- Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
| | - Klara Kirsch
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
| | - Hobin Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892
| | - Paola Oliva
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892
| | - Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
| | - Harsha Ravishankar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
| | - Stephen D. Fox
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD21702
| | - Samuel A. Kirby
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892
| | - Pooja Badhwar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD21702
| | - Kenneth A. Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892
| | - Kyung S. Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD20892
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3
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Stafford JM, Wyatt MD, McInnes C. Inhibitors of the PLK1 polo-box domain: drug design strategies and therapeutic opportunities in cancer. Expert Opin Drug Discov 2023; 18:65-81. [PMID: 36524399 DOI: 10.1080/17460441.2023.2159942] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Polo Like Kinase 1 (PLK1) is a key regulator of mitosis and its overexpression is frequently observed in a wide variety of human cancers, while often being associated with poor survival rates. Therefore, it is considered a potential and attractive target for cancer therapeutic development. The Polo like kinase family is characterized by the presence of a unique C terminal polobox domain (PBD) involved in regulating kinase activity and subcellular localization. Among the two functionally essential, druggable sites with distinct properties that PLK1 offers, targeting the PBD presents an alternative approach for therapeutic development. AREAS COVERED Significant progress has been made in progressing from the peptidic PBD inhibitors first identified, to peptidomimetic and recently drug-like small molecules. In this review, the rationale for targeting the PBD over the ATP binding site is discussed, along with recent progress, challenges, and outlook. EXPERT OPINION The PBD has emerged as a viable alternative target for the inhibition of PLK1, and progress has been made in using compounds to elucidate mechanistic aspects of activity regulation and in determining roles of the PBD. Studies have resulted in proof of concept of in vivo efficacy suggesting promise for PBD binders in clinical development.
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Affiliation(s)
- Jessy M Stafford
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Michael D Wyatt
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
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4
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Hymel D, Tsuji K, Grant RA, Chingle RM, Kunciw DL, Yaffe MB, Burke TR. Design and synthesis of a new orthogonally protected glutamic acid analog and its use in the preparation of high affinity polo-like kinase 1 polo-box domain - binding peptide macrocycles. Org Biomol Chem 2021; 19:7843-7854. [PMID: 34346472 PMCID: PMC8456285 DOI: 10.1039/d1ob01120k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022]
Abstract
Targeting protein - protein interactions (PPIs) has emerged as an important area of discovery for anticancer therapeutic development. In the case of phospho-dependent PPIs, such as the polo-like kinase 1 (Plk1) polo-box domain (PBD), a phosphorylated protein residue can provide high-affinity recognition and binding to target protein hot spots. Developing antagonists of the Plk1 PBD can be particularly challenging if one relies solely on interactions within and proximal to the phospho-binding pocket. Fortunately, the affinity of phospho-dependent PPI antagonists can be significantly enhanced by taking advantage of interactions in both the phospho-binding site and hidden "cryptic" pockets that may be revealed on ligand binding. In our current paper, we describe the design and synthesis of macrocyclic peptide mimetics directed against the Plk1 PBD, which are characterized by a new glutamic acid analog that simultaneously serves as a ring-closing junction that provides accesses to a cryptic binding pocket, while at the same time achieving proper orientation of a phosphothreonine (pT) residue for optimal interaction in the signature phospho-binding pocket. Macrocycles prepared with this new amino acid analog introduce additional hydrogen-bonding interactions not found in the open-chain linear parent peptide. It is noteworthy that this new glutamic acid-based amino acid analog represents the first example of extremely high affinity ligands where access to the cryptic pocket from the pT-2 position is made possible with a residue that is not based on histidine. The concepts employed in the design and synthesis of these new macrocyclic peptide mimetics should be useful for further studies directed against the Plk1 PBD and potentially for ligands directed against other PPI targets.
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Affiliation(s)
- David Hymel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Kohei Tsuji
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Robert A Grant
- Department of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ramesh M Chingle
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Dominique L Kunciw
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Michael B Yaffe
- Department of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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5
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Koehl P, Delarue M, Orland H. Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach. J Phys Chem B 2021; 125:5052-5067. [PMID: 33973782 DOI: 10.1021/acs.jpcb.1c02658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions between charges are controlled by electrostatics, while hydrophobic interactions are modeled with a Yukawa potential. We impose steric constraints by assuming that the system is represented on a cubic lattice. We also assume incompressibility; i.e., all sites of the lattice are occupied. This model, which we refer to as the Hydrophobic Dipolar Poisson-Boltzmann Langevin (HDPBL) model, leads to a system of two equations whose solutions give the water dipole, salt, and hydrophobic molecule densities, all of them in the presence of the others in a self-consistent way. We use those to study the organization of the ions, cosolvent, and solvent molecules around proteins. In particular, peaks of densities are expected to reveal, simultaneously, the presence of compatible binding sites of different kinds on a protein. We have tested and validated the ability of HDPBL to detect pockets in proteins that bind to hydrophobic ligands, polar ligands, and charged small probes as well as to characterize the binding sites of lipids for membrane proteins.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, United States
| | - Marc Delarue
- Architecture et Dynamique des Macromolécules Biologiques, Département de Biologie Structurale et Chimie, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, Université Paris-Saclay, CEA, 91191 Gif/Yvette Cedex, France
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6
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Bansia H, Mahanta P, Yennawar NH, Ramakumar S. Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches. J Chem Inf Model 2021; 61:1322-1333. [PMID: 33570386 DOI: 10.1021/acs.jcim.0c01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cryptic pockets are visible in ligand-bound protein structures but are occluded in unbound structures. Utilizing these pockets in fragment-based drug-design provides an attractive option for proteins not tractable by classical binding sites. However, owing to their hidden nature, they are difficult to identify. Here, we show that small glycols find cryptic pockets on a diverse set of proteins. Initial crystallography experiments serendipitously revealed the ability of ethylene glycol, a small glycol, to identify a cryptic pocket on the W6A mutant of the RBSX protein (RBSX-W6A). Explicit-solvent molecular dynamics (MD) simulations of RBSX-W6A with the exposed state of the cryptic pocket (ethylene glycol removed) revealed closure of the pocket reiterating that the exposed state of cryptic pockets in general are unstable in the absence of ligands. Also, no change in the pocket was observed for simulations of RBSX-W6A with the occluded state of the cryptic pocket, suggesting that water molecules are not able to open the cryptic pocket. "Cryptic-pocket finding" potential of small glycols was then supported and generalized through additional crystallography experiments, explicit-cosolvent MD simulations, and protein data set construction and analysis. The cryptic pocket on RBSX-W6A was found again upon repeating the crystallography experiments with another small glycol, propylene glycol. Use of ethylene glycol as a probe molecule in cosolvent MD simulations led to the enhanced sampling of the exposed state of experimentally observed cryptic sites on a test set of two proteins (Niemann-Pick C2, Interleukin-2). Further, analyses of protein structures with validated cryptic sites showed that ethylene glycol molecules bind to sites on proteins (Bcl-xL, G-actin, myosin II, and glutamate receptor 2), which become apparent upon binding of biologically relevant ligands. Our study thus suggests potential application of the small glycols in experimental and computational fragment-based approaches to identify cryptic pockets in apparently undruggable and/or difficult targets, making these proteins amenable to drug-design strategies.
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Affiliation(s)
- Harsh Bansia
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Pranjal Mahanta
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
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7
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Ripka JF, Perez-Riba A, Chaturbedy PK, Itzhaki LS. Testing the length limit of loop grafting in a helical repeat protein. Curr Res Struct Biol 2020; 3:30-40. [PMID: 34235484 PMCID: PMC8244534 DOI: 10.1016/j.crstbi.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Alpha-helical repeat proteins such as consensus-designed tetratricopeptide repeats (CTPRs) are exceptionally stable molecules that are able to tolerate destabilizing sequence alterations and are therefore becoming increasingly valued as a modular platform for biotechnology and biotherapeutic applications. A simple approach to functionalize the CTPR scaffold that we are pioneering is the insertion of short linear motifs (SLiMs) into the loops between adjacent repeats. Here, we test the limits of the scaffold by inserting 17 highly diverse amino acid sequences of up to 58 amino acids in length into a two-repeat protein and examine the impact on protein folding, stability and solubility. The sequences include three SLiMs that bind oncoproteins and eleven naturally occurring linker sequences all predicted to be intrinsically disordered but with conformational preferences ranging from compact globules to expanded coils. We show that the loop-grafted proteins retain the native CTPR structure and are thermally stable with melting temperatures above 60 °C, despite the longest loop sequence being almost the same size as the CTPR scaffold itself (68 amino acids). Although the main determinant of the effect of stability was found to be loop length and was relatively insensitive to amino acid composition, the relationship between protein solubility and the loop sequences was more complex, with the presence of negatively charged amino acids enhancing the solubility. Our findings will help us to fully realize the potential of the repeat-protein scaffold, allowing a rational design approach to create artificial modular proteins with customized functional capabilities.
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Key Words
- CD, circular dichroism
- CTPRs, consensus-designed tetratricopeptide repeats
- FCR, fraction of charged residues
- IDPs, intrinsically disordered proteins
- IDRs, intrinsically disordered regions
- Intrinsically disordered protein
- Intrinsically disordered region
- NCPR, net charge per residue
- PBIP1, polo-box interacting protein 1
- Peptide grafting
- SLiMs, short linear motifs
- TBP, tankyrase-binding peptides
- Tandem-repeat protein
- Tetratricopeptide repeat
- ves, effective solvation volume
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Affiliation(s)
- Juliane F. Ripka
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Piyush K. Chaturbedy
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Laura S. Itzhaki
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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8
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Cordeiro MH, Smith RJ, Saurin AT. Kinetochore phosphatases suppress autonomous Polo-like kinase 1 activity to control the mitotic checkpoint. J Cell Biol 2020; 219:e202002020. [PMID: 33125045 PMCID: PMC7608062 DOI: 10.1083/jcb.202002020] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/20/2020] [Accepted: 10/12/2020] [Indexed: 01/04/2023] Open
Abstract
Local phosphatase regulation is needed at kinetochores to silence the mitotic checkpoint (a.k.a. spindle assembly checkpoint [SAC]). A key event in this regard is the dephosphorylation of MELT repeats on KNL1, which removes SAC proteins from the kinetochore, including the BUB complex. We show here that PP1 and PP2A-B56 phosphatases are primarily required to remove Polo-like kinase 1 (PLK1) from the BUB complex, which can otherwise maintain MELT phosphorylation in an autocatalytic manner. This appears to be their principal role in the SAC because both phosphatases become redundant if PLK1 is inhibited or BUB-PLK1 interaction is prevented. Surprisingly, MELT dephosphorylation can occur normally under these conditions even when the levels or activities of PP1 and PP2A are strongly inhibited at kinetochores. Therefore, these data imply that kinetochore phosphatase regulation is critical for the SAC, but primarily to restrain and extinguish autonomous PLK1 activity. This is likely a conserved feature of the metazoan SAC, since the relevant PLK1 and PP2A-B56 binding motifs have coevolved in the same region on MADBUB homologues.
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Affiliation(s)
| | | | - Adrian T. Saurin
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
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9
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Tan YS, Verma CS. Straightforward Incorporation of Multiple Ligand Types into Molecular Dynamics Simulations for Efficient Binding Site Detection and Characterization. J Chem Theory Comput 2020; 16:6633-6644. [PMID: 32810406 DOI: 10.1021/acs.jctc.0c00405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Binding site identification and characterization is an important initial step in structure-based drug design. To account for the effects of protein flexibility and solvation, several cosolvent molecular dynamics (MD) simulation methods that incorporate small organic molecules into the protein's solvent box to probe for binding sites have been developed. However, most of these methods are highly inefficient, as they allow for the use of only one probe type at a time, which means that multiple sets of simulations have to be performed to map different types of binding sites. The high probe concentrations used in some of these methods also necessitate the use of artificial repulsive forces to prevent the probes from aggregating. Here, we present multiple-ligand-mapping MD (mLMMD), a method that incorporates multiple types of probes for simultaneous and efficient mapping of different types of binding sites without the need for introduction of artificial forces that may cause unintended mapping artifacts. We validate the method on a diverse set of 10 proteins and show that the mLMMD probes are able to reliably identify hydrophobic, hydrogen-bonding, charged, and cryptic binding sites in all of the test cases. Our results also highlight the potential utility of mLMMD for virtual screening and rational drug design.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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10
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Huggins DJ, Hardwick BS, Sharma P, Emery A, Laraia L, Zhang F, Narvaez AJ, Roberts-Thomson M, Crooks AT, Boyle RG, Boyce R, Walker DW, Mateu N, McKenzie GJ, Spring DR, Venkitaraman AR. Development of a Novel Cell-Permeable Protein-Protein Interaction Inhibitor for the Polo-box Domain of Polo-like Kinase 1. ACS OMEGA 2020; 5:822-831. [PMID: 31956833 PMCID: PMC6964520 DOI: 10.1021/acsomega.9b03626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/13/2019] [Indexed: 05/10/2023]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator of mitosis and a recognized drug target for cancer therapy. Inhibiting the polo-box domain of PLK1 offers potential advantages of increased selectivity and subsequently reduced toxicity compared with targeting the kinase domain. However, many if not all existing polo-box domain inhibitors have been shown to be unsuitable for further development. In this paper, we describe a novel compound series, which inhibits the protein-protein interactions of PLK1 via the polo-box domain. We combine high throughput screening with molecular modeling and computer-aided design, synthetic chemistry, and cell biology to address some of the common problems with protein-protein interaction inhibitors, such as solubility and potency. We use molecular modeling to improve the solubility of a hit series with initially poor physicochemical properties, enabling biophysical and biochemical characterization. We isolate and characterize enantiomers to improve potency and demonstrate on-target activity in both cell-free and cell-based assays, entirely consistent with the proposed binding model. The resulting compound series represents a promising starting point for further progression along the drug discovery pipeline and a new tool compound to study kinase-independent PLK functions.
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Affiliation(s)
- David J. Huggins
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
- TCM
Group, Cavendish Laboratory, University
of Cambridge, 19 JJ Thomson
Avenue, Cambridge CB3 0HE, United Kingdom
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Bryn S. Hardwick
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - Pooja Sharma
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - Amy Emery
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - Luca Laraia
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Fengzhi Zhang
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Ana J. Narvaez
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - Meredith Roberts-Thomson
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - Alex T. Crooks
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - Robert G. Boyle
- Sentinel
Oncology Ltd., Cambridge Science Park, Milton Road, Cambridge CB4 0EY, United Kingdom
| | - Richard Boyce
- Sentinel
Oncology Ltd., Cambridge Science Park, Milton Road, Cambridge CB4 0EY, United Kingdom
| | - David W. Walker
- Sentinel
Oncology Ltd., Cambridge Science Park, Milton Road, Cambridge CB4 0EY, United Kingdom
| | - Natalia Mateu
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Grahame J. McKenzie
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - David R. Spring
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Ashok R. Venkitaraman
- Medical
Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
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11
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Yan F, Liu G, Chen T, Fu X, Niu MM. Structure-Based Virtual Screening and Biological Evaluation of Peptide Inhibitors for Polo-Box Domain. Molecules 2019; 25:E107. [PMID: 31892137 PMCID: PMC6982974 DOI: 10.3390/molecules25010107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022] Open
Abstract
The polo-box domain of polo-like kinase 1 (PLK1-PBD) is proved to have crucial roles in cell proliferation. Designing PLK1-PBD inhibitors is challenging due to their poor cellular penetration. In this study, we applied a virtual screening workflow based on a combination of structure-based pharmacophore modeling with molecular docking screening techniques, so as to discover potent PLK1-PBD peptide inhibitors. The resulting 9 virtual screening peptides showed affinities for PLK1-PBD in a competitive binding assay. In particular, peptide 5 exhibited an approximately 100-fold increase in inhibitory activity (IC50 = 70 nM), as compared with the control poloboxtide. Moreover, cell cycle experiments indicated that peptide 5 effectively inhibited the expression of p-Cdc25C and cell cycle regulatory proteins by affecting the function of PLK1-PBD, thereby inducing mitotic arrest at the G2/M phase. Overall, peptide 5 can serve as a potent lead for further investigation as PLK1-PBD inhibitors.
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Affiliation(s)
| | | | | | | | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (F.Y.); (G.L.); (T.C.); (X.F.)
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12
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Zhou Y, Yan F, Huo X, Niu MM. Discovery of a Potent PLK1-PBD Small-Molecule Inhibitor as an Anticancer Drug Candidate through Structure-Based Design. Molecules 2019; 24:E4351. [PMID: 31795214 PMCID: PMC6930574 DOI: 10.3390/molecules24234351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/29/2022] Open
Abstract
Polo-box domain of polo-like kinase 1 (PLK1-PBD) has a pivotal role in cell proliferation and could be implicated as a potential anticancer target. Although some small-molecule inhibitors have been developed, their clinical application has been restricted by the poor selectivity. Therefore, there is an urgent need to develop effective PLK1-PBD inhibitors. Herein, we have developed a virtual screening protocol to find PLK1-PBD inhibitors by using combination of structure-based pharmacophore modeling and molecular docking. This protocol was successfully applied to screen PLK1-PBD inhibitors from specs database. MTT assay indicated that five screened hits suppressed the growth of HeLa cells. Particularly, hit-5, as a selective PLK1 inhibitor targeting PLK1-PBD, significantly inhibited the progression of HeLa cells-derived xenograft, with no obvious side effects. This work demonstrates that hit-5 may be a potential anticancer agent.
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Affiliation(s)
- Yunjiang Zhou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Yan
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
| | - Xiangyun Huo
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
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13
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Sharma P, Mahen R, Rossmann M, Stokes JE, Hardwick B, Huggins DJ, Emery A, Kunciw DL, Hyvönen M, Spring DR, McKenzie GJ, Venkitaraman AR. A cryptic hydrophobic pocket in the polo-box domain of the polo-like kinase PLK1 regulates substrate recognition and mitotic chromosome segregation. Sci Rep 2019; 9:15930. [PMID: 31685831 PMCID: PMC6828814 DOI: 10.1038/s41598-019-50702-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 07/26/2019] [Indexed: 11/25/2022] Open
Abstract
The human polo-like kinase PLK1 coordinates mitotic chromosome segregation by phosphorylating multiple chromatin- and kinetochore-binding proteins. How PLK1 activity is directed to specific substrates via phosphopeptide recognition by its carboxyl-terminal polo-box domain (PBD) is poorly understood. Here, we combine molecular, structural and chemical biology to identify a determinant for PLK1 substrate recognition that is essential for proper chromosome segregation. We show that mutations ablating an evolutionarily conserved, Tyr-lined pocket in human PLK1 PBD trigger cellular anomalies in mitotic progression and timing. Tyr pocket mutations selectively impair PLK1 binding to the kinetochore phosphoprotein substrate PBIP1, but not to the centrosomal substrate NEDD1. Through a structure-guided approach, we develop a small-molecule inhibitor, Polotyrin, which occupies the Tyr pocket. Polotyrin recapitulates the mitotic defects caused by mutations in the Tyr pocket, further evidencing its essential function, and exemplifying a new approach for selective PLK1 inhibition. Thus, our findings support a model wherein substrate discrimination via the Tyr pocket in the human PLK1 PBD regulates mitotic chromosome segregation to preserve genome integrity.
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Affiliation(s)
- Pooja Sharma
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom
| | - Robert Mahen
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom
| | - Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Jamie E Stokes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Bryn Hardwick
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom
| | - David J Huggins
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Amy Emery
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom
| | - Dominique L Kunciw
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Grahame J McKenzie
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom
| | - Ashok R Venkitaraman
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom.
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14
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Zhao XZ, Tsuji K, Hymel D, Burke TR. Development of Highly Selective 1,2,3-Triazole-containing Peptidic Polo-like Kinase 1 Polo-box Domain-binding Inhibitors. Molecules 2019; 24:E1488. [PMID: 31014020 PMCID: PMC6515314 DOI: 10.3390/molecules24081488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 01/02/2023] Open
Abstract
Members of the polo-like kinase (Plk) family of serine/threonine protein kinases play crucial roles in cell cycle regulation and proliferation. Of the five Plks (Plk1-5), Plk1 is recognized as an anticancer drug target. Plk1 contains multiple structural components that are important for its proper biological function. These include an N-terminal catalytic domain and a C-terminal non-catalytic polo-box domain (PBD). The PBD binds to phosphothreonine (pT) and phosphoserine-containing sequences. Blocking PBD-dependent interactions offers a potential means of down-regulating Plk1 function that is distinct from targeting its ATP-binding site. Previously, we demonstrated by tethering alkylphenyl chains from the N(π)-position of the His residue in the 5-mer PLHSpT, that we were able to access a hydrophobic "cryptic" binding pocket on the surface of the PBD, and in so doing enhance binding affinities by approximately 1000-fold. More recently, we optimized these PBD-ligand interactions using an oxime ligation-based strategy. Herein, using azide-alkyne cycloaddition reactions, we explore new triazole-containing PBD-binding antagonists. Some of these ligands retain the high PBD-binding affinity of the parent peptide, while showing desirable enhanced selectivity for the PBD of Plk1 relative to the PBDs of Plk2 and Plk3.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Kohei Tsuji
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - David Hymel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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15
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Rubner S, Schubert S, Berg T. Poloxin-2HT+: changing the hydrophobic tag of Poloxin-2HT increases Plk1 degradation and apoptosis induction in tumor cells. Org Biomol Chem 2019; 17:3113-3117. [PMID: 30848278 DOI: 10.1039/c9ob00080a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report the hydrophobically-tagged Plk1 PBD inhibitor Poloxin-2HT+, which selectively degrades the tumor target Plk1 and induces apoptosis in human tumor cells with higher potency than the hydrophobically-tagged inhibitor Poloxin-2HT. Our data provide further evidence that hydrophobically tagged inhibitors of protein-protein interactions can target and destroy disease-relevant proteins.
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Affiliation(s)
- Stefan Rubner
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103 Leipzig, Germany.
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16
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Lin TY, Min HP, Jiang C, Niu MM, Yan F, Xu LL, Di B. Design, synthesis and biological evaluation of phosphopeptides as Polo-like kinase 1 Polo-box domain inhibitors. Bioorg Med Chem 2018; 26:3429-3437. [PMID: 29807699 DOI: 10.1016/j.bmc.2018.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 10/16/2022]
Abstract
Polo-like kinase 1 (Plk1) is an anti-cancer target due to its critical role in mitotic progression. A growing body of evidence has documented that Peptide-Plk1 inhibitors showed high Plk1 binding affinity. However, phosphopeptides-Plk1 inhibitors showed poor cell membranes permeability, which limits their clinical applications. In current study, nine candidate phosphopeptides consisting of non-natural amino acids were rationally designed and then successfully synthesized using an Fmoc-solid phase peptide synthesis (SPPS) strategy. Moreover, the binding affinities and selectivity were evaluated via fluorescence polarization (FP) assay. The results confirmed that the most promising phosphopeptide 6 bound to Plk1 PBD with the IC50 of 38.99 nM, which was approximately 600-fold selectivity over Plk3 PBD (IC50 = 25.44 μM) and nearly no binding to Plk2 PBD. Furthermore the intracellular activities and the cell membrane permeability of phosphopeptide 6 were evalutated. Phosphopeptide 6 demonstrated appropriate cell membrane permeability and arrested HeLa cells cycle in G2/M phase by regulating CyclinB1-CDK1. Further, phosphopeptide 6 showed typical apoptotic morphology and induced caspase-dependent apoptosis. In conclusion, we expect our discovery can provide new insights into the further optimization of Plk1 PBD inhibitors.
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Affiliation(s)
- Tong-Yuan Lin
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Hong-Ping Min
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Cheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Miao-Miao Niu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Yan
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China.
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China.
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17
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Śledź P, Caflisch A. Protein structure-based drug design: from docking to molecular dynamics. Curr Opin Struct Biol 2017; 48:93-102. [PMID: 29149726 DOI: 10.1016/j.sbi.2017.10.010] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 01/24/2023]
Abstract
Recent years have witnessed rapid developments of computer-aided drug design methods, which have reached accuracy that allows their routine practical applications in drug discovery campaigns. Protein structure-based methods are useful for the prediction of binding modes of small molecules and their relative affinity. The high-throughput docking of up to 106 small molecules followed by scoring based on implicit-solvent force field can robustly identify micromolar binders using a rigid protein target. Molecular dynamics with explicit solvent is a low-throughput technique for the characterization of flexible binding sites and accurate evaluation of binding pathways, kinetics, and thermodynamics. In this review we highlight recent advancements in applications of ligand docking tools and molecular dynamics simulations to ligand identification and optimization.
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Affiliation(s)
- Paweł Śledź
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
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18
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Zhao XZ, Hymel D, Burke TR. Enhancing polo-like kinase 1 selectivity of polo-box domain-binding peptides. Bioorg Med Chem 2017; 25:5041-5049. [PMID: 28285924 PMCID: PMC5573662 DOI: 10.1016/j.bmc.2017.02.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
An important goal in the development of polo-like kinase 1 (Plk1) polo-box domain (PBD) binding inhibitors is selectivity for Plk1 relative to Plk2 and Plk3. In our current work we show that Plk1 PBD selectivity can be significantly enhanced by modulating interactions within a previously discovered "cryptic pocket" and a more recently identified proximal "auxiliary pocket."
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - David Hymel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States.
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19
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He D, Huang L, Xu Y, Pan X, Liu L. Molecular dynamics directed rational design and fluorescence binding assay of phosphopeptide ligands for PLK polo-box domain. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1244605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Deyong He
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an, P.R. China
| | - Ling Huang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an, P.R. China
| | - Yaping Xu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an, P.R. China
| | - Xiaoliang Pan
- School of Mechanical Engineering, Jinggangshan University, Ji’an, P.R. China
| | - Lijun Liu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an, P.R. China
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20
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Oleinikovas V, Saladino G, Cossins BP, Gervasio FL. Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations. J Am Chem Soc 2016; 138:14257-14263. [PMID: 27726386 DOI: 10.1021/jacs.6b05425] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cryptic pockets, that is, sites on protein targets that only become apparent when drugs bind, provide a promising alternative to classical binding sites for drug development. Here, we investigate the nature and dynamical properties of cryptic sites in four pharmacologically relevant targets, while comparing the efficacy of various simulation-based approaches in discovering them. We find that the studied cryptic sites do not correspond to local minima in the computed conformational free energy landscape of the unliganded proteins. They thus promptly close in all of the molecular dynamics simulations performed, irrespective of the force-field used. Temperature-based enhanced sampling approaches, such as Parallel Tempering, do not improve the situation, as the entropic term does not help in the opening of the sites. The use of fragment probes helps, as in long simulations occasionally it leads to the opening and binding to the cryptic sites. Our observed mechanism of cryptic site formation is suggestive of an interplay between two classical mechanisms: induced-fit and conformational selection. Employing this insight, we developed a novel Hamiltonian Replica Exchange-based method "SWISH" (Sampling Water Interfaces through Scaled Hamiltonians), which combined with probes resulted in a promising general approach for cryptic site discovery. We also addressed the issue of "false-positives" and propose a simple approach to distinguish them from druggable cryptic pockets. Our simulations, whose cumulative sampling time was more than 200 μs, help in clarifying the molecular mechanism of pocket formation, providing a solid basis for the choice of an efficient computational method.
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21
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Zhao XZ, Hymel D, Burke TR. Application of oxime-diversification to optimize ligand interactions within a cryptic pocket of the polo-like kinase 1 polo-box domain. Bioorg Med Chem Lett 2016; 26:5009-5012. [PMID: 27624074 PMCID: PMC5061138 DOI: 10.1016/j.bmcl.2016.08.098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 12/15/2022]
Abstract
By a process involving initial screening of a set of 87 aldehydes using an oxime ligation-based strategy, we were able to achieve a several-fold affinity enhancement over one of the most potent previously known polo-like kinase 1 (Plk1) polo-box domain (PBD) binding inhibitors. This improved binding may result by accessing a newly identified auxiliary region proximal to a key hydrophobic cryptic pocket on the surface of the protein. Our findings could have general applicability to the design of PBD-binding antagonists.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - David Hymel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States.
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22
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Mao XL, Wang KF, Zhu F, Pan ZH, Wu GM, Zhu HY. Rational Molecular Design of Potent PLK1 PBD Domain-binding Phosphopeptides Using Preferential Amino Acid Building Blocks. Chem Biodivers 2016; 13:1103-10. [PMID: 27450535 DOI: 10.1002/cbdv.201500513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 03/22/2016] [Indexed: 11/06/2022]
Abstract
Polo-like kinase 1 (PLK1) is an important regulator in diverse aspects of the cell cycle and proliferation. The protein has a highly conserved polo-box domain (PBD) present in C-terminal noncatalytic region, which exhibits a relatively broad sequence specificity in recognizing and binding phosphorylated substrates to control substrate phosphorylation by the kinase. In order to elucidate the structural basis, thermodynamic property, and biological implication underlying PBD-substrate recognition and association, a systematic amino acid preference profile of phosphopeptide interaction with PLK1 PBD domain was established via virtual mutagenesis analysis and mutation energy calculation, from which the contribution of different amino acids at each residue position of two reference phosphopeptides to domain-peptide binding was characterized comprehensively and quantitatively. With the profile, we are able to determine the favorable, neutral, and unfavorable amino acid types for each position of PBD-binding phosphopeptides, and we also explored the molecular origin of the broad sequence specificity in PBD-substrate recognition. To practice computational findings, the profile was further employed to guide rational design of potent PBD binders; three 6-mer phosphopeptides (i.e., IQSpSPC, LQSpTPF, and LNSpTPT) were successfully developed, which can efficiently target PBD domain with high affinity (Kd = 5.7 ± 1.1, 0.75 ± 0.18, and 7.2 ± 2.6 μm, resp.) as measured by a fluorescence anisotropy assay. The complex structure of PLK1 PBD domain with a newly designed, potent phosphopeptide LQSpTPF as well as diverse noncovalent chemical forces, such as H-bonds and hydrophobic interactions at the complex interface, were examined in detail to reveal the molecular mechanism of high affinity and stability of the complex system.
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Affiliation(s)
- Xin-Li Mao
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, P. R. China
| | - Kui-Feng Wang
- Department of Infectious Disease, Taizhou Hospital of Zhejiang Province, Linhai, 317000, P. R. China
| | - Feng Zhu
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, P. R. China
| | - Zhao-Hu Pan
- Department of Otorhinolaryngology, Taizhou Hospital of Zhejiang Province, No. 150 Ximen Str., Linhai, 317000, P. R. China
| | - Guo-Min Wu
- Department of Otorhinolaryngology, Taizhou Hospital of Zhejiang Province, No. 150 Ximen Str., Linhai, 317000, P. R. China
| | - Hong-Yuan Zhu
- Department of Otorhinolaryngology, Taizhou Hospital of Zhejiang Province, No. 150 Ximen Str., Linhai, 317000, P. R. China.
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23
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Zhu K, Shan Z, Zhang L, Wen W. Phospho-Pon Binding-Mediated Fine-Tuning of Plk1 Activity. Structure 2016; 24:1110-9. [PMID: 27238966 DOI: 10.1016/j.str.2016.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/29/2016] [Accepted: 04/25/2016] [Indexed: 01/08/2023]
Abstract
In Drosophila neuroblasts (NBs), the asymmetrical localization and segregation of the cell-fate determinant Numb are regulated by its adaptor Partner of Numb (Pon) and the cell-cycle kinase Polo. Polo phosphorylates the Pon localization domain, thus leading to its basal distribution together with Numb, albeit through an unclear mechanism. Here, we find that Cdk1 phosphorylates Pon at Thr63, thus creating a docking site for the Polo-box domain (PBD) of Polo-like kinase 1 (Plk1). The crystal structure of the Plk1 PBD/phospho-Pon complex reveals that two phospho-Pon bound PBDs associate to form a dimer of dimers. We provide evidence that phospho-Pon binding-induced PBD dimerization relieves the autoinhibition of Plk1. Moreover, we demonstrate that the priming Cdk1 phosphorylation of Pon is important for sequential Plk1 phosphorylation. Our results not only provide structural insight into how phosphoprotein binding activates Plk1 but also suggest that binding to different phosphoproteins might mediate the fine-tuning of Plk1 activity.
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Affiliation(s)
- Kang Zhu
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Zelin Shan
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Lu Zhang
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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24
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Dube D, Tiwari P, Kaur P. The hunt for antimitotic agents: an overview of structure-based design strategies. Expert Opin Drug Discov 2016; 11:579-97. [PMID: 27077683 DOI: 10.1080/17460441.2016.1174689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Structure-based drug discovery offers a rational approach for the design and development of novel anti-mitotic agents which target specific proteins involved in mitosis. This strategy has paved the way for development of a new generation of chemotypes which selectively interfere with the target proteins. The interference of these anti-mitotic targets implicated in diverse stages of mitotic cell cycle progression culminates in cancer cell apoptosis. AREAS COVERED This review covers the various mitotic inhibitors developed against validated mitotic checkpoint protein targets using structure-based design and optimization strategies. The protein-ligand interactions and the insights gained from these studies, culminating in the development of more potent and selective inhibitors, have been presented. EXPERT OPINION The advent of structure-based drug design coupled with advances in X-ray crystallography has revolutionized the discovery of candidate lead molecules. The structural insights gleaned from the co-complex protein-drug interactions have provided a new dimension in the design of anti-mitotic molecules to develop drugs with a higher selectivity and specificity profile. Targeting non-catalytic domains has provided an alternate approach to address cross-reactivity and broad selectivity among kinase inhibitors. The elucidation of structures of emerging mitotic drug targets has opened avenues for the design of inhibitors that target cancer.
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Affiliation(s)
- D Dube
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Tiwari
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Kaur
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
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25
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Scharow A, Knappe D, Reindl W, Hoffmann R, Berg T. Development of Bifunctional Inhibitors of Polo-Like Kinase 1 with Low-Nanomolar Activities Against the Polo-Box Domain. Chembiochem 2016; 17:759-67. [PMID: 26634982 DOI: 10.1002/cbic.201500535] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 01/10/2023]
Abstract
Polo-like kinase 1 (Plk1), a validated cancer target, harbors a protein-protein interaction domain referred to as the polo-box domain (PBD), in addition to its enzymatic domain. Although functional inhibition either of the enzymatic domain or of the PBD has been shown to inhibit Plk1, so far there have been no reports of bifunctional agents with the potential to target both protein domains. Here we report the development of Plk1 inhibitors that incorporate both an ATP-competitive ligand of the enzymatic domain, derived from BI 2536, and a functional inhibitor of the PBD, based either on the small molecule poloxin-2 or on a PBD-binding peptide. Although these bifunctional agents do not seem to bind both protein domains simultaneously, the most potent compound displays low-nanomolar activity against the Plk1 PBD, with excellent selectivity over the PBDs of Plk2 and Plk3. Our data provide insights into challenges and opportunities relating to the optimization of Plk1 PBD ligands as potent Plk1 inhibitors.
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Affiliation(s)
- Andrej Scharow
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Daniel Knappe
- Leipzig University, Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Wolfgang Reindl
- Max Planck Institute of Biochemistry, Department of Molecular Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419, Hamburg, Germany
| | - Ralf Hoffmann
- Leipzig University, Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Thorsten Berg
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany.
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Abstract
Polo-like kinase 1 (Plk1), a key player in mitosis, is overexpressed in a wide range of tumor types and has been validated as a target for tumor therapy. In addition to its N-terminal kinase domain, Plk1 harbors a C-terminal protein-protein interaction domain, referred to as the polo-box domain (PBD). Because the PBD is unique to the five-member family of polo-like kinases, and its inhibition is sufficient to inhibit the enzyme, the Plk1 PBD is an attractive target for the inhibition of Plk1 function. Although peptide-based inhibitors are invaluable tools for elucidating the nature of the binding interface, small molecules are better suited for the induction of mitotic arrest and apoptosis in tumor cells by Plk1 inhibition. This review describes the considerable progress that has been made in developing small-molecule and peptide-based inhibitors of the Plk1 PBD.
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Affiliation(s)
- Angela Berg
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Thorsten Berg
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany.
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Scott DE, Bayly AR, Abell C, Skidmore J. Small molecules, big targets: drug discovery faces the protein–protein interaction challenge. Nat Rev Drug Discov 2016; 15:533-50. [DOI: 10.1038/nrd.2016.29] [Citation(s) in RCA: 625] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Bakail M, Ochsenbein F. Targeting protein–protein interactions, a wide open field for drug design. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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29
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Lee KS, Burke TR, Park JE, Bang JK, Lee E. Recent Advances and New Strategies in Targeting Plk1 for Anticancer Therapy. Trends Pharmacol Sci 2015; 36:858-877. [PMID: 26478211 PMCID: PMC4684765 DOI: 10.1016/j.tips.2015.08.013] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/21/2015] [Accepted: 08/21/2015] [Indexed: 12/11/2022]
Abstract
Polo-like kinase 1 (Plk1) plays key roles in regulating mitotic processes that are crucial for cellular proliferation. Overexpression of Plk1 is tightly associated with the development of particular cancers in humans, and a large body of evidence suggests that Plk1 is an attractive target for anticancer therapeutic development. Drugs targeting Plk1 can potentially be directed at two distinct sites: the N-terminal catalytic kinase domain (KD), which phosphorylates substrates, and the C-terminal polo-box domain (PBD) which is essential for protein-protein interactions. In this review we summarize recent advances and new challenges in the development of Plk1 inhibitors targeting these two domains. We also discuss novel strategies for designing and developing next-generation inhibitors to effectively treat Plk1-associated human disorders.
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Affiliation(s)
- Kyung S Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeong K Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, 804-1, Yangcheong Ri, Ochang, Chungbuk, Cheongwon 363-883, Republic of Korea
| | - Eunhye Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Scharow A, Raab M, Saxena K, Sreeramulu S, Kudlinzki D, Gande S, Dötsch C, Kurunci-Csacsko E, Klaeger S, Kuster B, Schwalbe H, Strebhardt K, Berg T. Optimized Plk1 PBD Inhibitors Based on Poloxin Induce Mitotic Arrest and Apoptosis in Tumor Cells. ACS Chem Biol 2015; 10:2570-9. [PMID: 26279064 DOI: 10.1021/acschembio.5b00565] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polo-like kinase 1 (Plk1) is a central regulator of mitosis and has been validated as a target for antitumor therapy. The polo-box domain (PBD) of Plk1 regulates its kinase activity and mediates the subcellular localization of Plk1 and its interactions with a subset of its substrates. Functional inhibition of the Plk1 PBD by low-molecular weight inhibitors has been shown to represent a viable strategy by which to inhibit the enzyme, while avoiding selectivity issues caused by the conserved nature of the ATP binding site. Here, we report structure-activity relationships and mechanistic analysis for the first reported Plk1 PBD inhibitor, Poloxin. We present the identification of the optimized analog Poloxin-2, displaying significantly improved potency and selectivity over Poloxin. Poloxin-2 induces mitotic arrest and apoptosis in cultured human tumor cells at low micromolar concentrations, highlighting it as a valuable tool compound for exploring the function of the Plk1 PBD in living cells.
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Affiliation(s)
- Andrej Scharow
- Institute of Organic Chemistry, University of Leipzig , Johannisallee 29, 04103 Leipzig, Germany
| | - Monika Raab
- Johann Wolfgang Goethe-University , Medical School, Department of Gynecology and Obstetrics, Theodor-Stern-Kai 7-9, 60596 Frankfurt, Germany
| | - Krishna Saxena
- Johann Wolfgang Goethe-University Frankfurt , Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Sridhar Sreeramulu
- Johann Wolfgang Goethe-University Frankfurt , Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Denis Kudlinzki
- Johann Wolfgang Goethe-University Frankfurt , Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Santosh Gande
- Johann Wolfgang Goethe-University Frankfurt , Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Christina Dötsch
- Johann Wolfgang Goethe-University , Medical School, Department of Gynecology and Obstetrics, Theodor-Stern-Kai 7-9, 60596 Frankfurt, Germany
| | - Elisabeth Kurunci-Csacsko
- Johann Wolfgang Goethe-University , Medical School, Department of Gynecology and Obstetrics, Theodor-Stern-Kai 7-9, 60596 Frankfurt, Germany
| | - Susan Klaeger
- Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Bernhard Kuster
- Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Harald Schwalbe
- Johann Wolfgang Goethe-University Frankfurt , Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Klaus Strebhardt
- Johann Wolfgang Goethe-University , Medical School, Department of Gynecology and Obstetrics, Theodor-Stern-Kai 7-9, 60596 Frankfurt, Germany
- German Cancer Consortium (DKTK) , Heidelberg, Germany
| | - Thorsten Berg
- Institute of Organic Chemistry, University of Leipzig , Johannisallee 29, 04103 Leipzig, Germany
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31
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Archambault V, Lépine G, Kachaner D. Understanding the Polo Kinase machine. Oncogene 2015; 34:4799-807. [PMID: 25619835 DOI: 10.1038/onc.2014.451] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/27/2014] [Accepted: 11/28/2014] [Indexed: 12/26/2022]
Abstract
The Polo Kinase is a central regulator of cell division required for several events of mitosis and cytokinesis. In addition to a kinase domain (KD), Polo-like kinases (Plks) comprise a Polo-Box domain (PBD), which mediates protein interactions with targets and regulators of Plks. In all organisms that contain Plks, one Plk family member fulfills several essential functions in the regulation of cell division, and here we refer to this conserved protein as Polo Kinase (Plk1 in humans). The PBD and the KD are capable of both cooperation and mutual inhibition in their functions. Crystal structures of the PBD, the KD and, recently, a PBD-KD complex have helped understanding the inner workings of the Polo Kinase. In parallel, an impressive array of molecular mechanisms has been found to mediate the regulation of the protein. Moreover, the targeting of Polo Kinase in the development of anti-cancer drugs has yielded several molecules with which to chemically modulate Polo Kinase to study its biological functions. Here we review our current understanding of the protein function and regulation of Polo Kinase as a fascinating molecular device in control of cell division.
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Affiliation(s)
- V Archambault
- Institut de recherche en immunologie et en cancérologie, Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - G Lépine
- Institut de recherche en immunologie et en cancérologie, Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - D Kachaner
- Institut de recherche en immunologie et en cancérologie, Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec, Canada
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32
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Arquint C, Gabryjonczyk AM, Imseng S, Böhm R, Sauer E, Hiller S, Nigg EA, Maier T. STIL binding to Polo-box 3 of PLK4 regulates centriole duplication. eLife 2015; 4. [PMID: 26188084 PMCID: PMC4530586 DOI: 10.7554/elife.07888] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/17/2015] [Indexed: 01/14/2023] Open
Abstract
Polo-like kinases (PLK) are eukaryotic regulators of cell cycle progression, mitosis and cytokinesis; PLK4 is a master regulator of centriole duplication. Here, we demonstrate that the SCL/TAL1 interrupting locus (STIL) protein interacts via its coiled-coil region (STIL-CC) with PLK4 in vivo. STIL-CC is the first identified interaction partner of Polo-box 3 (PB3) of PLK4 and also uses a secondary interaction site in the PLK4 L1 region. Structure determination of free PLK4-PB3 and its STIL-CC complex via NMR and crystallography reveals a novel mode of Polo-box-peptide interaction mimicking coiled-coil formation. In vivo analysis of structure-guided STIL mutants reveals distinct binding modes to PLK4-PB3 and L1, as well as interplay of STIL oligomerization with PLK4 binding. We suggest that the STIL-CC/PLK4 interaction mediates PLK4 activation as well as stabilization of centriolar PLK4 and plays a key role in centriole duplication.
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Affiliation(s)
| | | | | | - Raphael Böhm
- Biozentrum, University of Basel, Basel, Switzerland
| | - Evelyn Sauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Erich A Nigg
- Biozentrum, University of Basel, Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
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33
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Kim JH, Ku B, Lee KS, Kim SJ. Structural analysis of the polo-box domain of human Polo-like kinase 2. Proteins 2015; 83:1201-8. [PMID: 25846005 PMCID: PMC7720676 DOI: 10.1002/prot.24804] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/03/2015] [Accepted: 03/20/2015] [Indexed: 12/25/2022]
Abstract
Polo-like kinases (Plks) are the key regulators of cell cycle progression, the members of which share a kinase domain and a polo-box domain (PBD) that serves as a protein-binding module. While Plk1 is a promising target for antitumor therapy, Plk2 is regarded as a tumor suppressor even though the two Plks commonly recognize the S-pS/T-P motif through their PBD. Herein, we report the crystal structure of the PBD of Plk2 at 2.7 Å. Despite the overall structural similarity with that of Plk1 reflecting their high sequence homology, the crystal structure also contains its own features including the highly ordered loop connecting two subdomains and the absence of 310 -helices in the N-terminal region unlike the PBD of Plk1. Based on the three-dimensional structure, we furthermore could model its interaction with two types of phosphopeptides, one of which was previously screened as the optimal peptide for the PBD of Plk2.
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Affiliation(s)
- Ju Hee Kim
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Bonsu Ku
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Kyung S. Lee
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Seung Jun Kim
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
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34
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Fischer G, Rossmann M, Hyvönen M. Alternative modulation of protein-protein interactions by small molecules. Curr Opin Biotechnol 2015; 35:78-85. [PMID: 25935873 PMCID: PMC4728186 DOI: 10.1016/j.copbio.2015.04.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/05/2023]
Abstract
Protein–protein interactions can be modulated by more than orthosteric disruption. Modulator categories: ‘orthosteric versus allosteric’ and ‘disrupting versus stabilising’. Interfacial binders exert secondary effects. Non-competitive modulation is a way around low affinity molecules. Non-competitive modulators require tailored screening strategies.
Protein–protein interactions (PPI) have become increasingly popular drug targets, with a number of promising compounds currently in clinical trials. Recent research shows, that PPIs can be modulated in more ways than direct inhibition, where novel non-competitive modes of action promise a solution for the difficult nature of PPI drug discovery. Here, we review recently discovered PPI modulators in light of their mode of action and categorise them as disrupting versus stabilising, orthosteric versus allosteric and by their ability to affect the proteins’ dynamics. We also give recent examples of compounds successful in the clinic, analyse their physicochemical properties and discuss how to overcome the hurdles in discovering alternative modes of modulation.
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Affiliation(s)
- Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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Shan HM, Shi Y, Quan J. Identification of green tea catechins as potent inhibitors of the polo-box domain of polo-like kinase 1. ChemMedChem 2015; 10:158-63. [PMID: 25196850 DOI: 10.1002/cmdc.201402284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 12/21/2022]
Abstract
Polo-like kinase 1 (PLK1) plays crucial functions in multiple stages of mitosis and is considered to be a potential drug target for cancer therapy. The functions of PLK1 are mediated by its N-terminal kinase domain and C-terminal polo-box domain (PBD). Most inhibitors targeting the kinase domain of PLK1 have a selectivity issue because of a high degree of structural conservation within kinase domains of all protein kinases. Here, we combined virtual and experimental screenings to identify green tea catechins as potent inhibitors of the PLK1 PBD. Initially, (-)-epigallocatechin, one of the main components of green tea polyphenols, was found to significantly block the binding of fluorescein-labeled phosphopeptide to the PBD at a concentration of 10 μm. Next, additional catechins were evaluated for their dose-dependent inhibition of the PBD and preliminary structure-activity relationships were derived. Cellular analysis further showed that catechins interfere with the proper subcellular localization of PLK1, lead to cell-cycle arrest in the S and G2M phases, and induce growth inhibition of several human cancer cell types, such as breast adenocarcinoma (MCF7), lung adenocarcinoma (A549), and cervical adenocarcinoma (HeLa). Our data provides new insight into understanding the anticancer activities of green tea catechins.
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Affiliation(s)
- Hong-Mei Shan
- Key Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055 (China)
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36
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Shan HM, Wang T, Quan JM. Crystal structure of the polo-box domain of polo-like kinase 2. Biochem Biophys Res Commun 2014; 456:780-4. [PMID: 25511705 DOI: 10.1016/j.bbrc.2014.11.125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 11/25/2014] [Indexed: 11/19/2022]
Abstract
Polo-like kinase 2 (PLK2) is a crucial regulator in cell cycle progression, DNA damage response, and neuronal activity. PLK2 is characterized by the conserved N-terminal kinase domain and the unique C-terminal polo-box domain (PBD). The PBD mediates diverse functions of PLK2 by binding phosphorylated Ser-pSer/pThr motifs of its substrates. Here, we report the first crystal structure of the PBD of PLK2. The overall structure of the PLK2 PBD is similar to that of the PLK1 PBD, which is composed by two polo boxes each contain β6α structures that form a 12-stranded β sandwich domain. The edge of the interface between the two polo boxes forms the phosphorylated Ser-pSer/pThr motifs binding cleft. On the hand, the peripheral regions around the core binding cleft of the PLK2 PBD is distinct from that of the PLK1 PBD, which might confer the substrate specificity of the PBDs of the polo-like kinase family.
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Affiliation(s)
- Hong-Mei Shan
- Key Laboratory of Structural Biology, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tao Wang
- Laboratory for Computational Chemistry & Drug Design, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China.
| | - Jun-Min Quan
- Key Laboratory of Structural Biology, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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37
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Qian WJ, Park JE, Lim D, Lai CC, Kelley JA, Park SY, Lee KW, Yaffe MB, Lee KS, Burke TR. Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high Plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in HeLa cells. Biopolymers 2014; 102:444-55. [PMID: 25283071 PMCID: PMC4895914 DOI: 10.1002/bip.22569] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/12/2014] [Accepted: 09/27/2014] [Indexed: 11/07/2022]
Abstract
Binding of polo-like kinase 1 (Plk1) polo-box domains (PBDs) to phosphothreonine (pThr)/phosphoserine (pSer)-containing sequences is critical for the proper function of Plk1. Although high-affinity synthetic pThr-containing peptides provide starting points for developing PBD-directed inhibitors, to date the efficacy of such peptides in whole cell assays has been poor. This potentially reflects limited cell membrane permeability arising, in part, from the di-anionic nature of the phosphoryl group or its mimetics. In our current article we report the unanticipated on-resin N(τ)-alkylation of histidine residues already bearing a N(π)- alkyl group. This resulted in cationic imidazolium-containing pThr peptides, several of which exhibit single-digit nanomolar PBD-binding affinities in extracellular assays and improved antimitotic efficacies in intact cells. We enhanced the cellular efficacies of these peptides further by applying bio-reversible pivaloyloxymethyl (POM) phosphoryl protection. New structural insights presented in our current study, including the potential utility of intramolecular charge masking, may be useful for the further development of PBD-binding peptides and peptide mimetics.
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Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Dan Lim
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Christopher C. Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - James A. Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - Suk-Youl Park
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
| | - Ki-Won Lee
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
- World Class University Biomodulation Major and Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Michael B. Yaffe
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
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Srinivasrao G, Park JE, Kim S, Ahn M, Cheong C, Nam KY, Gunasekaran P, Hwang E, Kim NH, Shin SY, Lee KS, Ryu E, Bang JK. Design and synthesis of a cell-permeable, drug-like small molecule inhibitor targeting the polo-box domain of polo-like kinase 1. PLoS One 2014; 9:e107432. [PMID: 25211362 PMCID: PMC4161390 DOI: 10.1371/journal.pone.0107432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/09/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Polo-like kinase-1 (Plk1) plays a crucial role in cell proliferation and the inhibition of Plk1 has been considered as a potential target for specific inhibitory drugs in anti-cancer therapy. Several research groups have identified peptide-based inhibitors that target the polo-box domain (PBD) of Plk1 and bind to the protein with high affinity in in vitro assays. However, inadequate proteolytic resistance and cell permeability of the peptides hinder the development of these peptide-based inhibitors into novel therapeutic compounds. METHODOLOGY/PRINCIPAL FINDINGS In order to overcome the shortcomings of peptide-based inhibitors, we designed and synthesized small molecule inhibitors. Among these molecules, bg-34 exhibited a high binding affinity for Plk1-PBD and it could cross the cell membrane in its unmodified form. Furthermore, bg-34-dependent inhibition of Plk1-PBD was sufficient for inducing apoptosis in HeLa cells. Moreover, modeling studies performed on Plk1-PBD in complex with bg-34 revealed that bg-34 can interact effectively with Plk1-PBD. CONCLUSION/SIGNIFICANCE We demonstrated that the molecule bg-34 is a potential drug candidate that exhibits anti-Plk1-PBD activity and possesses the favorable characteristics of high cell permeability and stability. We also determined that bg-34 induced apoptotic cell death by inhibiting Plk1-PBD in HeLa cells at the same concentration as PEGylated 4j peptide, which can inhibit Plk1-PBD activity 1000 times more effectively than bg-34 can in in vitro assays. This study may help to design and develop drug-like small molecule as Plk1-PBD inhibitor for better therapeutic activity.
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Affiliation(s)
- Ganipisetti Srinivasrao
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sungmin Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Chaejoon Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Ky-Youb Nam
- Institute for Innovative Cancer Research and Department of Convergence Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Pethaiah Gunasekaran
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Cheongju, Chung-Buk, Republic of Korea
| | - Eunha Hwang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Nam-Hyung Kim
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Cheongju, Chung-Buk, Republic of Korea
| | - Song Yub Shin
- Department of Bio-Materials, Graduate School and Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eunkyung Ryu
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
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39
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Sakkiah S, Senese S, Yang Q, Lee KW, Torres JZ. Dynamic and multi-pharmacophore modeling for designing polo-box domain inhibitors. PLoS One 2014; 9:e101405. [PMID: 25036740 PMCID: PMC4103762 DOI: 10.1371/journal.pone.0101405] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 06/06/2014] [Indexed: 02/04/2023] Open
Abstract
The polo-like kinase 1 (Plk1) is a critical regulator of cell division that is overexpressed in many types of tumors. Thus, a strategy in the treatment of cancer has been to target the kinase activity (ATPase domain) or substrate-binding domain (Polo-box Domain, PBD) of Plk1. However, only few synthetic small molecules have been identified that target the Plk1-PBD. Here, we have applied an integrative approach that combines pharmacophore modeling, molecular docking, virtual screening, and in vitro testing to discover novel Plk1-PBD inhibitors. Nine Plk1-PBD crystal structures were used to generate structure-based hypotheses. A common pharmacophore model (Hypo1) composed of five chemical features was selected from the 9 structure-based hypotheses and used for virtual screening of a drug-like database consisting of 159,757 compounds to identify novel Plk1-PBD inhibitors. The virtual screening technique revealed 9,327 compounds with a maximum fit value of 3 or greater, which were selected and subjected to molecular docking analyses. This approach yielded 93 compounds that made good interactions with critical residues within the Plk1-PBD active site. The testing of these 93 compounds in vitro for their ability to inhibit the Plk1-PBD, showed that many of these compounds had Plk1-PBD inhibitory activity and that compound Chemistry_28272 was the most potent Plk1-PBD inhibitor. Thus Chemistry_28272 and the other top compounds are novel Plk1-PBD inhibitors and could be used for the development of cancer therapeutics.
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Affiliation(s)
- Sugunadevi Sakkiah
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Silvia Senese
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Qianfan Yang
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, South Korea
| | - Jorge Z. Torres
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
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Murugan RN, Ahn M, Lee WC, Kim HY, Song JH, Cheong C, Hwang E, Seo JH, Shin SY, Choi SH, Park JE, Bang JK. Exploring the binding nature of pyrrolidine pocket-dependent interactions in the polo-box domain of polo-like kinase 1. PLoS One 2013; 8:e80043. [PMID: 24223211 PMCID: PMC3819306 DOI: 10.1371/journal.pone.0080043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/26/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Over the years, a great deal of effort has been focused on the design and synthesis of potent, linear peptide inhibitors targeting the polo-like kinase 1 (Plk1), which is critically involved in multiple mitotic processes and has been established as an adverse prognostic marker for tumor patients. Plk1 localizes to its intracellular anchoring sites via its polo-box domain, and inhibiting the Plk1 polo-box domain has been considered as an approach to circumvent the specificity problems associated with inhibiting the conserved adenosine triphosphate-binding pocket. The polo-box domain consists of two different binding regions, such as the unique, broader pyrrolidine-binding pocket and the conserved, narrow, Tyr-rich hydrophobic channel, among the three Plk polo-box domains (Plks 1-3), respectively. Therefore, the studies that provide insights into the binding nature of the unique, broader pyrrolidine-binding pocket might lead to the development of selective Plk1-inhibitory compounds. METHODOLOGY/PRINCIPAL FINDINGS In an attempt to retain the monospecificity by targeting the unique, broader pyrrolidine-binding pocket, here, for the first time, a systematic approach was undertaken to examine the structure-activity relationship of N-terminal-truncated PLHSpTM derivatives, to apply a site-directed ligand approach using bulky aromatic and non-aromatic systems, and to characterize the binding nature of these analogues using X-ray crystallographic studies. We have identified a new mode of binding interactions, having improved binding affinity and retaining the Plk1 polo-box domain specificity, at the pyrrolidine-binding pocket. Furthermore, our data revealed that the pyrrolidine-binding pocket was very specific to recognize a short and bulky hydrophobic ligand like adamantane, whereas the Tyr-rich hydrophobic channel was specific with lengthy and small hydrophobic groups. CONCLUSION/SIGNIFICANCE The progress made using our site-directed ligands validated this approach to specifically direct the ligand into the unique pyrrolidine-binding region, and it extends the applicability of the strategy for discovering selective protein-protein interaction inhibitors.
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Affiliation(s)
- Ravichandran N. Murugan
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Woo Cheol Lee
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Hye-Yeon Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Jung Hyun Song
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Chaejoon Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Eunha Hwang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Ji-Hyung Seo
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Song Yub Shin
- Department of Bio-Materials, Graduate School and Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sun Ho Choi
- Dong-A ST, Research Laboratories, YongIn, Gyeonggi-do, Republic of Korea
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
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41
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Abstract
This protocol describes the screening of a library of low-molecular-weight compounds (fragments) using a series of biophysical ligand-binding assays. Fragment-based drug discovery (FBDD) has emerged as a successful method to design high-affinity ligands for biomacromolecules of therapeutic interest. It involves detecting relatively weak interactions between the fragments and a target macromolecule using sensitive biophysical techniques. These weak binders provide a starting point for the development of inhibitors with submicromolar affinity. Here we describe an efficient fragment screening cascade that can identify binding fragments (hits) within weeks. It is divided into three stages: (i) preliminary screening using differential scanning fluorimetry (DSF), (ii) validation by NMR spectroscopy and (iii) characterization of binding fragments by isothermal titration calorimetry (ITC) and X-ray crystallography. Although this protocol is readily applicable in academic settings because of its emphasis on low cost and medium-throughput early-stage screening technologies, the core principle of orthogonal validation makes it robust enough to meet the quality standards of an industrial laboratory.
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42
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Qian WJ, Park JE, Lim D, Park SY, Lee KW, Yaffe MB, Lee KS, Burke TR. Peptide-based inhibitors of Plk1 polo-box domain containing mono-anionic phosphothreonine esters and their pivaloyloxymethyl prodrugs. CHEMISTRY & BIOLOGY 2013; 20:1255-64. [PMID: 24120332 PMCID: PMC3859306 DOI: 10.1016/j.chembiol.2013.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/19/2013] [Accepted: 09/04/2013] [Indexed: 12/11/2022]
Abstract
Binding of polo-like kinase 1 (Plk1) polo-box domains (PBDs) to phosphothreonine (pThr)/phosphoserine (pSer)-containing sequences is critical for the proper function of Plk1. Although high-affinity synthetic pThr-containing peptides may be used to disrupt PBD function, the efficacy of such peptides in whole cell assays has been poor. This potentially reflects limited cell membrane permeability arising in part from the di-anionic nature of the phosphoryl group. We report five-mer peptides containing mono-anionic pThr phosphoryl esters that exhibit single-digit nanomolar PBD binding affinities in extracellular assays and improved antimitotic efficacies in whole cell assays. The cellular efficacies of these peptides have been further enhanced by the application of bio-reversible pivaloyloxymethyl (POM) phosphoryl protection to a pThr-containing polypeptide. Our findings may redefine structural parameters for the development of PBD-binding peptides and peptide mimetics.
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Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, U. S. A
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Dan Lim
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Suk-Youl Park
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
| | - Ki -Won Lee
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
- World Class University Biomodulation Major and Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Michael B. Yaffe
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, U. S. A
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Xu J, Shen C, Wang T, Quan J. Structural basis for the inhibition of Polo-like kinase 1. Nat Struct Mol Biol 2013; 20:1047-53. [PMID: 23893132 DOI: 10.1038/nsmb.2623] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/30/2013] [Indexed: 01/29/2023]
Abstract
Polo-like kinase 1 (PLK1) is a master regulator of mitosis and is considered a potential drug target for cancer therapy. PLK1 is characterized by an N-terminal kinase domain (KD) and a C-terminal Polo-box domain (PBD). The KD and PBD are mutually inhibited, but the molecular mechanisms of the autoinhibition remain unclear. Here we report the 2.3-Å crystal structure of the complex of the Danio rerio KD and PBD together with a PBD-binding motif of Drosophila melanogaster microtubule-associated protein 205 (Map205(PBM)). The structure reveals that the PBD binds and rigidifies the hinge region of the KD in a distinct conformation from that of the phosphopeptide-bound PBD. This structure provides a framework for understanding the autoinhibitory mechanisms of PLK1 and also sheds light on the activation mechanisms of PLK1 by phosphorylation or phosphopeptide binding.
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Affiliation(s)
- Jun Xu
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
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44
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Matthews LA, Guarné A. Dbf4: the whole is greater than the sum of its parts. Cell Cycle 2013; 12:1180-8. [PMID: 23549174 PMCID: PMC3674083 DOI: 10.4161/cc.24416] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 03/22/2013] [Indexed: 12/29/2022] Open
Abstract
Together with cyclin-dependent kinases, the Dbf4-dependent kinase (DDK) is essential to activate the Mcm2-7 helicase and, hence, initiate DNA replication in eukaryotes. Beyond its role as the regulatory subunit of the DDK complex, the Dbf4 protein also regulates the activity of other cell cycle kinases to mediate the checkpoint response and prevent premature mitotic exit under stress. Two features that are unusual in DNA replication proteins characterize Dbf4. The first is its evolutionary divergence; the second is how its conserved motifs are combined to form distinct functional units. This structural plasticity appears to be at odds with the conserved functions of Dbf4. In this review, we summarize recent genetic, biochemical and structural work delineating the multiple interactions mediated by Dbf4 and its various functions during the cell cycle. We also discuss how the limited sequence conservation of Dbf4 may be an advantage to regulate the activities of multiple cell cycle kinases.
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Affiliation(s)
- Lindsay A Matthews
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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45
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Van Molle I, Thomann A, Buckley DL, So EC, Lang S, Crews CM, Ciulli A. Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. ACTA ACUST UNITED AC 2013; 19:1300-12. [PMID: 23102223 DOI: 10.1016/j.chembiol.2012.08.015] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 01/06/2023]
Abstract
Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed.
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Affiliation(s)
- Inge Van Molle
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
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46
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Qian WJ, Park JE, Lee KS, Burke TR. Non-proteinogenic amino acids in the pThr-2 position of a pentamer peptide that confer high binding affinity for the polo box domain (PBD) of polo-like kinase 1 (Plk1). Bioorg Med Chem Lett 2012; 22:7306-8. [PMID: 23159568 PMCID: PMC3530200 DOI: 10.1016/j.bmcl.2012.10.093] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/16/2012] [Accepted: 10/19/2012] [Indexed: 12/23/2022]
Abstract
We report herein that incorporating long-chain alkylphenyl-containing non-proteinogenic amino acids in place of His at the pT-2 position of the parent polo-like kinase 1 (Plk1) polo box domain (PBD)-binding pentapeptide, PLHSpT (1a) increases affinity. For certain analogs, approximately two orders-of-magnitude improvement in affinity was observed. Although, none of the new analogs was as potent as our previously described peptide 1b, in which the pT-2 histidine imidazole ring is alkylated at its π nitrogen (N3), our current finding that the isomeric His(N1)-analog (1c) binds with approximately 50-fold less affinity than 1b, indicates the positional importance of attachment to the His imidazole ring. Our demonstration that a range of modified residues at the pT-2 position can enhance binding affinity, should facilitate the development of minimally-sized Plk1 PBD-binding antagonists.
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Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, U. S. A
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, U. S. A
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47
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Maia AR, Garcia Z, Kabeche L, Barisic M, Maffini S, Macedo-Ribeiro S, Cheeseman IM, Compton DA, Kaverina I, Maiato H. Cdk1 and Plk1 mediate a CLASP2 phospho-switch that stabilizes kinetochore-microtubule attachments. J Cell Biol 2012; 199:285-301. [PMID: 23045552 PMCID: PMC3471233 DOI: 10.1083/jcb.201203091] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 09/17/2012] [Indexed: 11/22/2022] Open
Abstract
Accurate chromosome segregation during mitosis relies on a dynamic kinetochore (KT)-microtubule (MT) interface that switches from a labile to a stable condition in response to correct MT attachments. This transition is essential to satisfy the spindle-assembly checkpoint (SAC) and couple MT-generated force with chromosome movements, but the underlying regulatory mechanism remains unclear. In this study, we show that during mitosis the MT- and KT-associated protein CLASP2 is progressively and distinctively phosphorylated by Cdk1 and Plk1 kinases, concomitant with the establishment of KT-MT attachments. CLASP2 S1234 was phosphorylated by Cdk1, which primed CLASP2 for association with Plk1. Plk1 recruitment to KTs was enhanced by CLASP2 phosphorylation on S1234. This was specifically required to stabilize KT-MT attachments important for chromosome alignment and to coordinate KT and non-KT MT dynamics necessary to maintain spindle bipolarity. CLASP2 C-terminal phosphorylation by Plk1 was also required for chromosome alignment and timely satisfaction of the SAC. We propose that Cdk1 and Plk1 mediate a fine CLASP2 "phospho-switch" that temporally regulates KT-MT attachment stability.
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Affiliation(s)
- Ana R.R. Maia
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Zaira Garcia
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Lilian Kabeche
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755
- Norris Cotton Cancer Center, Lebanon, NH 03766
| | - Marin Barisic
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Stefano Maffini
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Iain M. Cheeseman
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Duane A. Compton
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755
- Norris Cotton Cancer Center, Lebanon, NH 03766
| | - Irina Kaverina
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Helder Maiato
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Department of Experimental Biology, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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48
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Tan YS, Śledź P, Lang S, Stubbs CJ, Spring DR, Abell C, Best RB. Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1. Angew Chem Int Ed Engl 2012; 51:10078-81. [PMID: 22961729 PMCID: PMC3547296 DOI: 10.1002/anie.201205676] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Yaw Sing Tan
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Paweł Śledź
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Steffen Lang
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Christopher J Stubbs
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - David R Spring
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Chris Abell
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Robert B Best
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
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49
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Tan YS, Śledź P, Lang S, Stubbs CJ, Spring DR, Abell C, Best RB. Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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50
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Śledź P, Lang S, Stubbs CJ, Abell C. High-throughput interrogation of ligand binding mode using a fluorescence-based assay. Angew Chem Int Ed Engl 2012; 51:7680-3. [PMID: 22730171 PMCID: PMC3556687 DOI: 10.1002/anie.201202660] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Indexed: 11/07/2022]
Abstract
Probing the pocket: A high-throughput fluorescence-based thermal shift (FTS) assay utilized different forms of a protein (in gray) to establish the binding mode of a ligand (see picture). The assay serves in the rapid evaluation of structure-activity binding-mode relationships for a series of ligands of Plk1, an important target of anticancer therapy.
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Affiliation(s)
- Paweł Śledź
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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