1
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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: 4] [Impact Index Per Article: 4.0] [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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2
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Wang HM, Seo CD, Lee KJ, Park JH, Lim HS. Evaluation of the cell permeability of bicyclic peptoids and bicyclic peptide-peptoid hybrids. Bioorg Chem 2022; 127:105976. [DOI: 10.1016/j.bioorg.2022.105976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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3
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Ryu S, Park JE, Ham YJ, Lim DC, Kwiatkowski NP, Kim DH, Bhunia D, Kim ND, Yaffe MB, Son W, Kim N, Choi TI, Swain P, Kim CH, Lee JY, Gray NS, Lee KS, Sim T. Novel Macrocyclic Peptidomimetics Targeting the Polo-Box Domain of Polo-Like Kinase 1. J Med Chem 2022; 65:1915-1932. [PMID: 35029981 PMCID: PMC10411393 DOI: 10.1021/acs.jmedchem.1c01359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The polo-box domain (PBD) of Plk1 is a promising target for cancer therapeutics. We designed and synthesized novel phosphorylated macrocyclic peptidomimetics targeting PBD based on acyclic phosphopeptide PMQSpTPL. The inhibitory activities of 16e on Plk1-PBD is >30-fold higher than those of PMQSpTPL. Both 16a and 16e possess excellent selectivity for Plk1-PBD over Plk2/3-PBD. Analysis of the cocrystal structure of Plk1-PBD in complex with 16a reveals that the 3-(trifluoromethyl)benzoyl group in 16a interacts with Arg516 through a π-stacking interaction. This π-stacking interaction, which has not been reported previously, provides insight into the design of novel and potent Plk1-PBD inhibitors. Furthermore, 16h, a PEGlyated macrocyclic phosphopeptide derivative, induces Plk1 delocalization and mitotic failure in HeLa cells. Also, the number of phospho-H3-positive cells in a zebrafish embryo increases in proportion to the amount of 16a. Collectively, the novel macrocyclic peptidomimetics should serve as valuable templates for the design of potent and novel Plk1-PBD inhibitors.
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Affiliation(s)
- SeongShick Ryu
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea; Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Young Jin Ham
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Daniel C. Lim
- Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P. Kwiatkowski
- Harvard Medical School, Boston, Massachusetts 02115, United States; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Do-Hee Kim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Chemistry, College of Convergence and Integrated Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Debabrata Bhunia
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Nam Doo Kim
- Voronoibio Inc., Incheon 21984, Republic of Korea
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States; Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Woolim Son
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Namkyoung Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea; Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Puspanjali Swain
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jin-Young Lee
- Department of Biological Sciences, Keimyung University, Daegu 42601, Republic of Korea
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of, Health, Bethesda, Maryland 20892, United States
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea; Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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4
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Samarasimhareddy M, Shamir M, Shalev DE, Hurevich M, Friedler A. A Rapid and Efficient Building Block Approach for Click Cyclization of Peptoids. Front Chem 2020; 8:405. [PMID: 32509731 PMCID: PMC7248394 DOI: 10.3389/fchem.2020.00405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Cyclic peptide-peptoid hybrids possess improved stability and selectivity over linear peptides and are thus better drug candidates. However, their synthesis is far from trivial and is usually difficult to automate. Here we describe a new rapid and efficient approach for the synthesis of click-based cyclic peptide-peptoid hybrids. Our methodology is based on a combination between easily synthesized building blocks, automated microwave assisted solid phase synthesis and bioorthogonal click cyclization. We proved the concept of this method using the INS peptide, which we have previously shown to activate the HIV-1 integrase enzyme. This strategy enabled the rapid synthesis and biophysical evaluation of a library of cyclic peptide-peptoid hybrids derived from HIV-1 integrase in high yield and purity. The new cyclic hybrids showed improved biological activity and were significantly more stable than the original linear INS peptide.
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Affiliation(s)
| | - Mai Shamir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deborah E Shalev
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Pharmaceutical Engineering, Azrieli College of Engineering Jerusalem, Jerusalem, Israel
| | - Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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5
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Choi JS, Joo SH. Recent Trends in Cyclic Peptides as Therapeutic Agents and Biochemical Tools. Biomol Ther (Seoul) 2020; 28:18-24. [PMID: 31597413 PMCID: PMC6939695 DOI: 10.4062/biomolther.2019.082] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/26/2022] Open
Abstract
Notable progress has been made in the therapeutic and research applications of cyclic peptides since our previous review. New drugs based on cyclic peptides are entering the market, such as plecanatide, a cyclic peptide approved by the United States Food and Drug Administration in 2017 for the treatment of chronic idiopathic constipation. In this review, we discuss recent developments in stapled peptides, prepared with the use of chemical linkers, and bicyclic/tricyclic peptides with more than two rings. These have widespread applications for clinical and research purposes: imaging, diagnostics, improvement of oral absorption, enzyme inhibition, development of receptor agonist/antagonist, and the modulation of protein-protein interaction or protein-RNA interaction. Many cyclic peptides are expected to emerge as therapeutics and biochemical tools.
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Affiliation(s)
- Joon-Seok Choi
- College of Pharmacy, Daegu Catholic University, Gyeongsan 38430, Republic of Korea
| | - Sang Hoon Joo
- College of Pharmacy, Daegu Catholic University, Gyeongsan 38430, Republic of Korea
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6
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Li Z, Zhang Z, Sun H, Xu L, Jiang C. Identification of novel peptidomimetics targeting the polo-box domain of polo-like kinase 1. Bioorg Chem 2019; 91:103148. [PMID: 31376784 DOI: 10.1016/j.bioorg.2019.103148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/09/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
A series of new peptidomimetics targeting the polo-box domain (PBD) of polo-like kinase 1 (Plk1) was identified based on the potent and selective pentapeptide Plk1 PBD inhibitor PLHSpT. Unnatural amino acid residues were introduced to the newly designed compound and the N-terminal substituent of the peptidomimetic was investigated. The optimized compound 9 inhibited the Plk1 PBD with IC50 of 0.267 μM and showed almost no inhibition to Plk2 PBD or Plk3 PBD at 100 μM. Biolayer interferometry studies demonstrated that compound 9 showed potent binding affinity to Plk1 with a Kd value of 0.164 μM, while no Kd were detected against Plk2 and Plk3. Compound 9 showed improved stability in rat plasma compared to PLHSpT. Binding mode analysis was performed and in agreement with the observed experimental results. There are only two natural amino acids remained in the chemical structure of 9. This study may provide new information for further research on Plk1 PBD inhibitors.
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Affiliation(s)
- Zhiyan Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Zhenguo Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Lili 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.
| | - Cheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China.
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7
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Ojo OS, Nardone B, Musolino SF, Neal AR, Wilson L, Lebl T, Slawin AMZ, Cordes DB, Taylor JE, Naismith JH, Smith AD, Westwood NJ. Synthesis of the natural product descurainolide and cyclic peptides from lignin-derived aromatics. Org Biomol Chem 2019; 16:266-273. [PMID: 29242868 DOI: 10.1039/c7ob02697h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Alternative sources of potential feedstock chemicals are of increasing importance as the availability of oil decreases. The biopolymer lignin is viewed as a source of useful mono-aromatic compounds as exemplified by the industrial scale production of vanillin from this biomass. Alternative lignin-derived aromatics are available in pure form but to date examples of the use of these types of compounds are rare. Here we address this issue by reporting the conversion of an aromatic keto-alcohol to the anti- and syn-isomers of Descurainolide A. The key step involves a rhodium-catalyzed allylic substitution reaction. Enantio-enriched allylic alcohols were generated via an isothiourea-catalyzed kinetic resolution enabling access to both the (2R,3R) and (2S,3S) enantiomers of anti-Descurainolide A. In addition we show that the lignin-derived keto-alcohols can be converted into unnatural amino acid derivatives of tyrosine. Finally, these amino acids were incorporated into cyclic peptide scaffolds through the use of both chemical and an enzyme-mediated macrocylisation.
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Affiliation(s)
- O Stephen Ojo
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, KY16 9ST, UK
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8
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Li Z, Zhang Z, Chen Y, Tang S, Lin T, Huang J, Li B, Jiang C. Design, synthesis and evaluation of d-amino acid-containing peptidomimetics targeting the polo-box domain of polo-like kinase 1. Bioorg Chem 2019; 85:534-540. [PMID: 30807896 DOI: 10.1016/j.bioorg.2019.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/27/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
A series of d-amino acid-containing peptidomimetics were designed, synthesized as novel polo-like kinase 1 (Plk1) polo-box domain (PBD) inhibitors based on the reported peptide Plk1 PBD inhibitor. Their inhibitory activity to Plk1, Plk2, and Plk3 PBD were evaluated using our fluorescence polarization (FP) assay. Compound 18 bound to Plk1 PBD with IC50 of 0.80 μM and showed nearly no inhibition to Plk2 PBD or Plk3 PBD at 100 μM. Compound 18 induced Hela cells to undergo apoptosis by increasing the ratio of the cells at the G2/M phase by decreasing the neosynthesized proteins in a dose-dependent manner from 50 to 150 μM. Compound 18 showed improved stability in rat plasma compared to l-peptide inhibitor LHSpTA. These novel d-amino acid modified selective Plk1 PBD inhibitors may provide new lead compounds for further optimization.
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Affiliation(s)
- Zhiyan Li
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Zhenguo Zhang
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Yanhong Chen
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Shijun Tang
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Tongyuan 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
| | - Jingfang Huang
- 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
| | - Bo Li
- 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; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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9
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Brahm K, Wack JS, Eckes S, Engemann V, Schmitz K. Macrocyclization enhances affinity of chemokine‐binding peptoids. Biopolymers 2018; 110:e23244. [DOI: 10.1002/bip.23244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Kevin Brahm
- Clemens‐Schöpf‐Institute of Organic Chemistry and BiochemistryTU Darmstadt Darmstadt Germany
| | - Julia S. Wack
- Clemens‐Schöpf‐Institute of Organic Chemistry and BiochemistryTU Darmstadt Darmstadt Germany
| | - Stefanie Eckes
- Clemens‐Schöpf‐Institute of Organic Chemistry and BiochemistryTU Darmstadt Darmstadt Germany
| | - Victoria Engemann
- Clemens‐Schöpf‐Institute of Organic Chemistry and BiochemistryTU Darmstadt Darmstadt Germany
| | - Katja Schmitz
- Clemens‐Schöpf‐Institute of Organic Chemistry and BiochemistryTU Darmstadt Darmstadt Germany
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10
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Chen Y, Li Z, Liu Y, Lin T, Sun H, Yang D, Jiang C. Identification of novel and selective non-peptide inhibitors targeting the polo-box domain of polo-like kinase 1. Bioorg Chem 2018; 81:278-288. [PMID: 30170276 DOI: 10.1016/j.bioorg.2018.08.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 01/05/2023]
Abstract
A series of non-peptide inhibitors targeting the polo-box domain (PBD) of polo-like kinase 1 (Plk1) was designed based on the potent and selective minimal tripeptide Plk1 PBD inhibitor. Seven compounds were designed, synthesized and evaluated for fluorescence polarization (FP) assay. The most promising compound 10 bound to Plk1 PBD with IC50 of 3.37 μM and had no binding to Plk2 PBD or Plk3 PBD at 100 μM. Molecular docking study was performed and possible binding mode was proposed. MM/GBSA binding free energy calculation were in agreement with the observed experimental results. These novel non-peptide selective Plk1 PBD inhibitors provided new lead compounds for further optimization.
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Affiliation(s)
- Yanhong Chen
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Zhiyan Li
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Yu Liu
- 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; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Tongyuan 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
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Dasong Yang
- 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; Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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11
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Hymel D, Grant RA, Tsuji K, Yaffe MB, Burke TR. Histidine N(τ)-cyclized macrocycles as a new genre of polo-like kinase 1 polo-box domain-binding inhibitors. Bioorg Med Chem Lett 2018; 28:3202-3205. [PMID: 30174151 PMCID: PMC6287497 DOI: 10.1016/j.bmcl.2018.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/06/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022]
Abstract
Transition toward peptide mimetics of reduced size is an important objective of peptide macrocyclization. We have previously shown that PLH∗SpT (2a) (where H∗ indicates the presence of a -(CH2)8Ph group at the N(π) position and pT indicates phosphothreonine) is an extremely high affinity ligand of the polo-like kinase 1 (Plk1) polo-box domain (PBD). Herein we report that C-terminal macrocyclization of 2a employing N(π),N(τ)-bis-alkylated His residues as ring junctions can be achieved in a very direct fashion. The resulting macrocycles are highly potent in biochemical assays and maintain good target selectivity for the Plk1 PBD versus the PBDs of Plk2 and Plk3. Importantly, as exemplified by 5d, our current approach permits deletion of the N-terminal "Pro-Leu" motif to yield tripeptide ligands with decreased molecular weight, which retain high affinity and show improved target selectivity. These findings could fundamentally impact the future development of peptide macrocycles in general and Plk1 PBD-binding peptide mimetics in particular.
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Affiliation(s)
- David Hymel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Robert A Grant
- Department of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kohei Tsuji
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, 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-Frederick, Frederick, MD 21702, USA.
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12
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Sun J, Liu HY, Xu RF, Zhu HL. Identification of nitroimidazole-oxime derivatives targeting the polo-box domain of polo-like kinase 1. Bioorg Med Chem 2017; 25:6581-6588. [PMID: 29100732 DOI: 10.1016/j.bmc.2017.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/15/2017] [Accepted: 10/25/2017] [Indexed: 11/23/2022]
Abstract
Recent progress in the development of small molecular skeleton-derived polo-like kinase (PLK1) catalytic domain (KD) inhibitors has led to the synthesis of multiple ligands with high binding affinity. However, few systematic analyses have been conducted to identify key PLK1-PBD domain and characterize their interactions with potent PLK1 inhibitors. Therefore, we designed a series of PLK1-PBD inhibitors with an in silico scaffold modification strategy. A docking simulation combined with a primary screen in vitro were performed to filter for the lead compound, which was then substituted, synthesized and evaluated by a variety of bioassays. The biological profile of 4v suggests that this compound may be developed as a potential anticancer agent.
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Affiliation(s)
- Juan Sun
- School of Life Sciences, Shandong University of Technology, Zibo 255049, PR China; Elion Nature Biological Technology Co., Ltd, Nanjing 210046, PR China.
| | - Han-Yu Liu
- School of Life Sciences, Shandong University of Technology, Zibo 255049, PR China
| | - Ruo-Fei Xu
- Shandong Experimental High School, Jinan 250001, PR China
| | - Hai-Liang Zhu
- Elion Nature Biological Technology Co., Ltd, Nanjing 210046, PR China
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13
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Park JE, Hymel D, Burke TR, Lee KS. Current progress and future perspectives in the development of anti-polo-like kinase 1 therapeutic agents. F1000Res 2017; 6:1024. [PMID: 28721210 PMCID: PMC5497816 DOI: 10.12688/f1000research.11398.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/23/2017] [Indexed: 12/21/2022] Open
Abstract
Although significant levels of side effects are often associated with their use, microtubule-directed agents that primarily target fast-growing mitotic cells have been considered to be some of the most effective anti-cancer therapeutics. With the hope of developing new-generation anti-mitotic agents with reduced side effects and enhanced tumor specificity, researchers have targeted various proteins whose functions are critically required for mitotic progression. As one of the highly attractive mitotic targets, polo-like kinase 1 (Plk1) has been the subject of an extensive effort for anti-cancer drug discovery. To date, a variety of anti-Plk1 agents have been developed, and several of them are presently in clinical trials. Here, we will discuss the current status of generating anti-Plk1 agents as well as future strategies for designing and developing more efficacious anti-Plk1 therapeutics.
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Affiliation(s)
- Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Hymel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Kyung S Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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14
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Gunasekaran P, Lee SR, Jeong SM, Kwon JW, Takei T, Asahina Y, Bang G, Kim S, Ahn M, Ryu EK, Kim HN, Nam KY, Shin SY, Hojo H, Namgoong S, Kim NH, Bang JK. Pyrrole-Based Macrocyclic Small-Molecule Inhibitors That Target Oocyte Maturation. ChemMedChem 2017; 12:580-589. [PMID: 28296169 DOI: 10.1002/cmdc.201700048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/13/2017] [Indexed: 11/08/2022]
Abstract
Polo-like kinase 1 (PLK1) plays crucial roles in various stages of oocyte maturation. Recently, we reported that the peptidomimetic compound AB103-8, which targets the polo box domain (PBD) of PLK1, affects oocyte meiotic maturation and the resumption of meiosis. However, to overcome the drawbacks of peptidic compounds, we designed and synthesized a series of pyrrole-based small-molecule inhibitors and tested them for their effects on the rates of porcine oocyte maturation. Among them, the macrocyclic compound (E/Z)-3-(2,16-dioxo-19-(4-phenylbutyl)-3,19-diazabicyclo[15.2.1]icosa-1(20),6,17-trien-3-yl)propyl dihydrogen phosphate (4) showed the highest inhibitory activity with enhanced inhibition against embryonic blastocyst formation. Furthermore, the addition of this compound to culture media efficiently blocked the maturation of porcine and mouse oocytes, indicating its ability to penetrate the zona pellucida and cell membrane. We investigated mouse oocytes treated with compound 4, and the resulting impairment of spindle formation confirmed PLK1 inhibition. Finally, molecular modeling studies with PLK1 PBD also confirmed the presence of significant interactions between compound 4 and PLK1 PBD binding pocket residues, including those in the phosphate, tyrosine-rich, and pyrrolidine binding pockets. Collectively, these results suggest that the macrocyclic compound 4 may serve as a promising template for the development of novel contraceptive agents.
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Affiliation(s)
- Pethaiah Gunasekaran
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Chung-Buk, 361-763, Republic of Korea
| | - So-Rim Lee
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Chung-Buk, 361-763, Republic of Korea
| | - Seung-Min Jeong
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Chung-Buk, 361-763, Republic of Korea
| | - Jeong-Woo Kwon
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Chung-Buk, 361-763, Republic of Korea
| | - Toshiki Takei
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuya Asahina
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Geul Bang
- Biomedical Omics Group, Korea Basic Science Institute, Ochang, Chung-Buk, 363-883, Republic of Korea
| | - Seongnyeon Kim
- Biomedical Omics Group, Korea Basic Science Institute, Ochang, Chung-Buk, 363-883, Republic of Korea
| | - Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, 363-883, Republic of Korea
| | - Eun Kyung Ryu
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, 363-883, Republic of Korea
- Department of Bio-analytical Science, University of Science & Technology, Daejeon, 34113, Republic of Korea
| | - Hak Nam Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, 363-883, Republic of Korea
| | - Ki-Yub Nam
- Pharos I&BT Co. Ltd., Gyeonggi-do, 14059, Republic of Korea
| | - Song Yub Shin
- Department of Medical Science, Graduate School and Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Suk Namgoong
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Chung-Buk, 361-763, Republic of Korea
| | - Nam-Hyung Kim
- Molecular Embryology Laboratory, Department of Animal Sciences, Chungbuk National University, Chung-Buk, 361-763, Republic of Korea
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, 363-883, Republic of Korea
- Department of Bio-analytical Science, University of Science & Technology, Daejeon, 34113, Republic of Korea
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15
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Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
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16
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Qian WJ, Park JE, Grant R, Lai CC, Kelley JA, Yaffe MB, Lee KS, Burke TR. Neighbor-directed histidine N (τ)-alkylation: A route to imidazolium-containing phosphopeptide macrocycles. Biopolymers 2016; 104:663-73. [PMID: 26152807 DOI: 10.1002/bip.22698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/15/2015] [Accepted: 07/04/2015] [Indexed: 12/24/2022]
Abstract
Our recently discovered, selective, on-resin route to N(τ)-alkylated imidazolium-containing histidine residues affords new strategies for peptide mimetic design. In this, we demonstrate the use of this chemistry to prepare a series of macrocyclic phosphopeptides, in which imidazolium groups serve as ring-forming junctions. Interestingly, these cationic moieties subsequently serve to charge-mask the phosphoamino acid group that directed their formation. Neighbor-directed histidine N(τ)-alkylation opens the door to new families of phosphopeptidomimetics for use in a range of chemical biology contexts.
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Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Robert Grant
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Christopher C Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| | - Michael B Yaffe
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Kyung S Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
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17
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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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18
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Furukawa A, Townsend CE, Schwochert J, Pye CR, Bednarek MA, Lokey RS. Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry. J Med Chem 2016; 59:9503-9512. [PMID: 27690434 DOI: 10.1021/acs.jmedchem.6b01246] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Synthetic and natural cyclic peptides provide a testing ground for studying membrane permeability in nontraditional drug scaffolds. Cyclic peptomers, which incorporate peptide and N-alkylglycine (peptoid) residues, combine the stereochemical and geometric complexity of peptides with the functional group diversity accessible to peptoids. We synthesized cyclic peptomer libraries by split-pool techniques, separately permuting side chain and backbone geometry, and analyzed their membrane permeabilities using the parallel artificial membrane permeability assay. Nearly half of the side chain permutations had permeability coefficients (Papp) > 1 × 10-6 cm/s. Some backbone geometries enhanced permeability due to their ability to form more stable intramolecular hydrogen bond networks compared with other scaffolds. These observations suggest that hexameric cyclic peptomers can have good passive permeability even in the context of extensive side chain and backbone variation, and that high permeability can generally be achieved within a relatively wide lipophilicity range.
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Affiliation(s)
- Akihiro Furukawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.,Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R Pye
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd. , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
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19
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DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization. Molecules 2016; 21:molecules21091082. [PMID: 27563857 PMCID: PMC6274049 DOI: 10.3390/molecules21091082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 11/17/2022] Open
Abstract
Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5'-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5'-C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected.
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20
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Butterfoss GL, Drew K, Renfrew PD, Kirshenbaum K, Bonneau R. Conformational preferences of peptide-peptoid hybrid oligomers. Biopolymers 2016; 102:369-78. [PMID: 24919990 DOI: 10.1002/bip.22516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/04/2014] [Accepted: 06/08/2014] [Indexed: 11/07/2022]
Abstract
Peptomers are oligomeric molecules composed of both α-amino acids and N-substituted glycine monomers, thus creating a hybrid of peptide and peptoid units. Peptomers have been used in several applications such as antimicrobials, protease inhibitors, and antibody mimics. Despite the considerable promise of peptomers as chemically diverse molecular scaffolds, we know little about their conformational tendencies. This lack of knowledge limits the ability to implement computational approaches for peptomer design. Here we computationally evaluate the local structural propensities of the peptide-peptoid linkage. We find some general similarities between the peptide residue conformational preferences and the Ramachandran distribution of residues that precede proline in folded protein structures. However, there are notable differences. For example, several β-turn motifs are disallowed when the i+2 residue is also a peptoid monomer. Significantly, the lowest energy geometry, when dispersion forces are accounted for, corresponds to a "cis-Pro touch-turn" conformation, an unusual turn motif that has been observed at protein catalytic centers and binding sites. The peptomer touch-turn thus represents a useful design element for the construction of folded oligomers capable of molecular recognition and as modules in the assembly of structurally complex peptoid-protein hybrid macromolecules.
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Affiliation(s)
- Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box, 129188, Abu Dhabi, United Arab Emirates
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21
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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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22
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Watanabe N, Osada H. Small molecules that target phosphorylation dependent protein-protein interaction. Bioorg Med Chem 2016; 24:3246-54. [PMID: 27017542 DOI: 10.1016/j.bmc.2016.03.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 12/12/2022]
Abstract
Protein-protein interaction is one of the key events in the signal transduction pathway. The interaction changes the conformations, activities, localization and stabilities of the proteins, and transduces the signal to the next step. Frequently, this interaction occurs upon the protein phosphorylation. When upstream signals are stimulated, protein kinase(s) is/are activated and phosphorylate(s) their substrates, and induce the phosphorylation dependent protein-protein interaction. For this interaction, several domains in proteins are known to specifically recognize the phosphorylated residues of target proteins. These specific domains for interaction are important in the progression of the diseases caused by disordered signal transduction such as cancer. Thus small molecules that modulate this interaction are attractive lead compounds for the treatment of such diseases. In this review, we focused on three examples of phosphorylation dependent protein-protein interaction modules (14-3-3, polo box domain of Plk1 and F-box proteins in SCF ubiquitin ligases) and summarize small molecules that modulate their interaction. We also introduce our original screening system to identify such small molecules.
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Affiliation(s)
- Nobumoto Watanabe
- Bio-Active Compounds Discovery Research Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Bio-Probe Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, Wako, Saitama 351-0198, Japan.
| | - Hiroyuki Osada
- Bio-Probe Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, Wako, Saitama 351-0198, Japan; Chemical Biology Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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23
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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24
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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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25
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Park JE, Kim TS, Meng L, Bang JK, Kim BY, Lee KS. Putting a bit into the polo-box domain of polo-like kinase 1. J Anal Sci Technol 2015; 6:27. [PMID: 26500787 PMCID: PMC4610673 DOI: 10.1186/s40543-015-0069-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/27/2015] [Indexed: 01/11/2023] Open
Abstract
Polo-like kinase 1 (Plk1) plays key roles in regulating various mitotic processes that are critical for cellular proliferation. A growing body of evidence suggests that Plk1 overexpression is tightly associated with the development of human cancers. Interestingly, various types of cancer cells are shown to be addicted to a high level of Plk1, and the reversal of Plk1 addiction appears to be an effective strategy for selectively killing cancer cells, but not normal cells. Therefore, Plk1 is considered an attractive anticancer drug target. Over the years, a large number of inhibitors that target the catalytic activity of Plk1 have been developed. However, these inhibitors exhibit significant levels of cross-reactivity with related kinases, including Plk2 and Plk3. Consequently, as an alternative approach for developing anti-Plk1 therapeutics, substantial effort is under way to develop inhibitors that target the C-terminal protein–protein interaction domain of Plk1, called the polo-box domain (PBD). In this communication, I will discuss the pros and cons of targeting the PBD in comparison to those of targeting the ATP-binding site within the kinase domain.
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Affiliation(s)
- Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 37, Room 3118, Bethesda, MD 20892 USA
| | - Tae-Sung Kim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 37, Room 3118, Bethesda, MD 20892 USA
| | - Lingjun Meng
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 37, Room 3118, Bethesda, MD 20892 USA
| | - Jeong K Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, 804-1, Yangcheong Ri, Ochang, 363-883 Chungbuk Republic of Korea
| | - Bo Y Kim
- World Class Institute, Korea Research Institute of Bioscience and Biotechnology, Ochang, 363-883 Republic of Korea
| | - Kyung S Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 37, Room 3118, Bethesda, MD 20892 USA
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26
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Jia JL, Han YH, Kim HC, Ahn M, Kwon JW, Luo Y, Gunasekaran P, Lee SJ, Lee KS, Kyu Bang J, Kim NH, Namgoong S. Structural basis for recognition of Emi2 by Polo-like kinase 1 and development of peptidomimetics blocking oocyte maturation and fertilization. Sci Rep 2015; 5:14626. [PMID: 26459104 PMCID: PMC4602232 DOI: 10.1038/srep14626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/01/2015] [Indexed: 11/08/2022] Open
Abstract
In a mammalian oocyte, completion of meiosis is suspended until fertilization by a sperm, and the cell cycle is arrested by a biochemical activity called cytostatic factor (CSF). Emi2 is one of the CSFs, and it maintains the protein level of maturation promoting factor (MPF) by inhibiting ubiquitin ligase anaphase promoting complex/cyclosome (APC/C). Degradation of Emi2 via ubiquitin-mediated proteolysis after fertilization requires phosphorylation by Polo-like kinase 1 (Plk1). Therefore, recognition and phosphorylation of Emi2 by Plk1 are crucial steps for cell cycle resumption, but the binding mode of Emi2 and Plk1 is poorly understood. Using biochemical assays and X-ray crystallography, we found that two phosphorylated threonines (Thr(152) and Thr(176)) in Emi2 are each responsible for the recruitment of one Plk1 molecule by binding to its C-terminal polo box domain (PBD). We also found that meiotic maturation and meiosis resumption via parthenogenetic activation were impaired when Emi2 interaction with Plk1-PBD was blocked by a peptidomimetic called 103-8. Because of the inherent promiscuity of kinase inhibitors, our results suggest that targeting PBD of Plk1 may be an effective strategy for the development of novel and specific contraceptive agents that block oocyte maturation and/or fertilization.
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Affiliation(s)
- Jia-Lin Jia
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
| | - Young-Hyun Han
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
| | - Hak-Cheol Kim
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
| | - Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Korea
| | - Jeong-Woo Kwon
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
| | - Yibo Luo
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
| | | | - Soo-Jae Lee
- College of Pharmacy, Chungbuk National University, Republic of Korea
| | - Kyung S. Lee
- National Cancer Institute, National Institute of Health, Rockville, Maryland, United States
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
| | - Suk Namgoong
- Department of Animal Sciences, Chungbuk National University, Republic of Korea
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27
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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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Liu M, Huang J, Chen DX, Jiang C. Identification of indole-3-carboxylic acids as non-ATP-competitive Polo-like kinase 1 (Plk1) inhibitors. Bioorg Med Chem Lett 2015; 25:431-4. [PMID: 25556101 DOI: 10.1016/j.bmcl.2014.12.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 12/02/2014] [Accepted: 12/18/2014] [Indexed: 12/31/2022]
Abstract
A series of indole-3-carboxylic acids were designed as novel small molecular non-ATP-competitive Plk1 inhibitors. The designed compounds were synthesized and evaluated. Most of the targeted compounds showed potent Plk1 inhibitory activities and anti-proliferative characters. Particularly, 4f and 4g showed Plk1 inhibitory activity with IC50 values of 0.41 and 0.13μM, which were about 5 and 17 times more potent compared to thymoquinone, respectively. Compound 4g also showed inhibitory activity to HeLa and MCF-7 cell lines with IC50 values of 0.72 and 1.15μM, which was almost 3 and 4 times more potent than thymoquinone. Study of mechanism of action suggested that 4g was an ATP-independent and substrate-dependent Plk1 inhibitor. Moreover, 4g showed excellent Plk1 inhibitory selectivity against Plk2 and Plk3. Fluorescein isothiocyanate Annexin V/propidium iodide (PI) double-staining assay and western-blot results indicate that induction of apoptosis by 4g is involved in its anti-tumor activity. This study may provide a support for further optimization of non-ATP-competitive Plk1 inhibitors.
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Affiliation(s)
- Meng Liu
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy,China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China
| | - Jie Huang
- Gansu Institute for Food and Drug Control, Yinan road 7, Lanzhou 730070, China
| | - Dong-Xing Chen
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy,China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China
| | - Cheng Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy,China Pharmaceutical University, Tongjiaxiang 24, Nanjing 210009, China.
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29
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Ahn M, Han YH, Park JE, Kim S, Lee WC, Lee SJ, Gunasekaran P, Cheong C, Shin SY, Kim HY, Ryu EK, Murugan RN, Kim NH, Bang JK. A new class of peptidomimetics targeting the polo-box domain of Polo-like kinase 1. J Med Chem 2015; 58:294-304. [PMID: 25347203 DOI: 10.1021/jm501147g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent progress in the development of peptide-derived Polo-like kinase (Plk1) polo-box domain (PBD) inhibitors has led to the synthesis of multiple peptide ligands with high binding affinity and selectivity. However, few systematic analyses have been conducted to identify key Plk1 residues and characterize their interactions with potent Plk1 peptide inhibitors. We performed systematic deletion analysis using the most potent 4j peptide and studied N-terminal capping of the minimal peptide with diverse organic moieties, leading to the identification of the peptidomimetic 8 (AB-103) series with high binding affinity and selectivity. To evaluate the bioavailability of short peptidomimetic ligands, PEGylated 8 series were synthesized and incubated with HeLa cells to test for cellular uptake, antiproliferative activity, and Plk1 kinase inhibition. Finally, crystallographic studies of the Plk1 PBD in complex with peptidomimetics 8 and 22 (AB-103-5) revealed the presence of two hydrogen bond interactions responsible for their high binding affinity and selectivity.
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Affiliation(s)
- Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute , 804-1, Yangcheong Ri, Ochang, Chungbuk, Cheongwon 363-883, Republic of Korea
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30
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Clède S, Delsuc N, Laugel C, Lambert F, Sandt C, Baillet-Guffroy A, Policar C. An easy-to-detect nona-arginine peptide for epidermal targeting. Chem Commun (Camb) 2015; 51:2687-9. [DOI: 10.1039/c4cc08737b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nona-arginine peptide conjugated with a Re-tricarbonyl IR and fluorescent probe (SCoMPI) accumulates at the epidermis without reaching the dermis.
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Affiliation(s)
- Sylvain Clède
- Ecole Normale Supérieure-PSL Research University
- Département de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- UMR 7203 CNRS-ENS-UPMC LBM
- 75005 Paris
| | - Nicolas Delsuc
- Ecole Normale Supérieure-PSL Research University
- Département de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- UMR 7203 CNRS-ENS-UPMC LBM
- 75005 Paris
| | - Cécile Laugel
- Laboratory of Analytical Chemistry
- Analytical Chemistry Group of Paris-Sud (GCAPS-EA 4041)
- Faculty of Pharmacy
- University Paris-Sud
- 92296 Chatenay-Malabry
| | - François Lambert
- Ecole Normale Supérieure-PSL Research University
- Département de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- UMR 7203 CNRS-ENS-UPMC LBM
- 75005 Paris
| | - Christophe Sandt
- Smis beamline
- Synchrotron SOLEIL Saint-Aubin
- Gif-sur-Yvette Cedex
- France
| | - Arlette Baillet-Guffroy
- Laboratory of Analytical Chemistry
- Analytical Chemistry Group of Paris-Sud (GCAPS-EA 4041)
- Faculty of Pharmacy
- University Paris-Sud
- 92296 Chatenay-Malabry
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Département de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- UMR 7203 CNRS-ENS-UPMC LBM
- 75005 Paris
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Chen DX, Huang J, Liu M, Xu YG, Jiang C. Design, synthesis, and evaluation of non-ATP-competitive small-molecule Polo-like kinase 1 (Plk1) inhibitors. Arch Pharm (Weinheim) 2015; 348:2-9. [PMID: 25430493 DOI: 10.1002/ardp.201400294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/11/2014] [Accepted: 10/17/2014] [Indexed: 02/04/2023]
Abstract
A series of small-molecule Plk1 inhibitors targeting the substrate-binding pocket were designed through rational drug design for the first time. The designed compounds were synthesized and their activities were evaluated in vitro. Some of the targeted compounds showed potent Plk1 inhibitory activities and anti-proliferative characters. Particularly, 5i showed Plk1 inhibitory activity with an IC50 value of 0.68 µM. Compound 5i also showed cell growth inhibitory activity on HeLa cells with an IC50 value of 0.51 µM, which is about four times more potent compared to thymoquinone. The mechanism of action suggested that 5i was an ATP-independent and substrate-dependent Plk1 inhibitor. Compound 5i demonstrated excellent Plk1 inhibitory selectivity against Plk2, Plk3, and five serine/threonine and tyrosine kinases. Our discovery and structure-activity relationship study may provide useful lead compounds for further optimization of non-ATP-competitive Plk1 inhibitors.
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Affiliation(s)
- Dong-Xing Chen
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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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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Structural features of peptoid-peptide hybrids in lipid-water interfaces. FEBS Lett 2014; 588:3291-7. [DOI: 10.1016/j.febslet.2014.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/24/2014] [Accepted: 07/14/2014] [Indexed: 12/15/2022]
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34
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Nam KY, Kang JH, No KT, Ahn SK. Identification of Polo-Like Kinase 1 Inhibitors Using Structure-Based Molecular Design. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.7.1929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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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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